GidA1

ABSTRACT

The invention provides gidA1 polypeptides and polynucleotides encoding gidA1 polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing gidA1 polypeptides to screen for antibacterial compounds.

RELATED APPLICATIONS

[0001] This application claims benefit of U.S. Provisional PatentApplication No. 60/051,379, filed Jul. 1, 1997.

FIELD OF THE INVENTION

[0002] This invention relates to newly identified polynucleotides andpolypeptides, and their production and uses, as well as their variants,agonists and antagonists, and their uses. In particular, the inventionrelates to polynucleotides and polypeptides of the gidA family, as wellas their variants, hereinafter referred to as “gidA1,” “gidA1polynucleotide(s),” and “gidA1 polypeptide(s)” as the case may be.

BACKGROUND OF THE INVENTION

[0003] The Streptococci make up a medically important genera of microbesknown to cause several types of disease in humans, including, forexample, otitis media, conjunctivitis, pneumonia, bacteremia,meningitis, sinusitis, pleural empyema and endocarditis, and mostparticularly meningitis, such as for example infection of cerebrospinalfluid. Since its isolation more than 100 years ago, Streptococcuspneumoniae has been one of the more intensively studied microbes. Forexample, much of our early understanding that DNA is, in fact, thegenetic material was predicated on the work of Griffith and of Aver,Macleod and McCarty using this microbe. Despite the vast amount ofresearch with S. pneumoniae, many questions concerning the virulence ofthis microbe remain. It is particularly preferred to employStreptococcal genes and gene products as targets for the development ofantibiotics.

[0004] The frequency of Streptococcus pneumoniae infections has risendramatically in the past few decades. This has been attributed to theemergence of multiply antibiotic resistant strains and an increasingpopulation of people with weakened immune systems. It is no longeruncommon to isolate Streptococcus pneumoniae strains which are resistantto some or all of the standard antibiotics. This phenomenon has createdan unmet medical need and demand for new anti-microbial agents,vaccines, drug screening methods, and diagnostic tests for thisorganism.

[0005] Moreover, the drug discovery process is currently undergoing afundamental revolution as it embraces “functional genomics,” that is,high throughput genome- or gene-based biology. This approach is rapidlysuperseding earlier approaches based on “positional cloning” and othermethods. Functional genomics relies heavily on the various tools ofbioinformatics to identify gene sequences of potential interest from themany molecular biology databases now available as well as from othersources. There is a continuing and significant need to identify andcharacterize further genes and other polynucleotides sequences and theirrelated polypeptides, as targets for drug discovery.

[0006] Clearly, there exists a need for polynucleotides andpolypeptides, such as the gidA1 embodiments of the invention, that havea present benefit of, among other things, being useful to screencompounds for antimicrobial activity. Such factors are also useful todetermine their role in pathogenesis of infection, dysfunction anddisease. There is also a need for identification and characterization ofsuch factors and their antagonists and agonists to find ways to prevent,ameliorate or correct such infection, dysfunction and disease. Certainof the polypeptides of the invention possess significant amino acidsequence homology to a known gidA protein. The first described gidA genewas that of E. coli (von Meyenburg et al (1980) ICN-UCLA Symp. Mol.Cell. Biol. 19, 137-159; Genbank accession number P17112). The closesthomolog of S. pneumoniae gidA1 is Lactococcus lactis gidA (Duwat, P. etal. (1997) J. Bacteriol. 179(14), 4473-79; Genbank accession number forpolynucleotide is U80409, and SwissProt accession number for polypeptideis 032806). Other references relating to bacterial gidA genes areOgasawara, N. & Yoshikawa, H. (1992) Mol. Microbiol. 6(5), 629-634, andKunst, F. et al. (1997) Nature 390, 249-256 (Bacillus subtilis gidA);Karita, M et al. (1997) Infection & Immunity 65(10), 4158-64(Helicobacter pylori gidA); Fsihi, H. et al. (1996) Microbiology142(11), 3147-61 (Mycobacterium leprae gidA).

SUMMARY OF THE INVENTION

[0007] The present invention relates to gidA1, in particular gidA1polypeptides and gidA1 polynucleotides, recombinant materials andmethods for their production. In another aspect, the invention relatesto methods for using such polypeptides and polynucleotides, includingtreatment of microbial diseases, amongst others. In a further aspect,the invention relates to methods for identifying agonists andantagonists using the materials provided by the invention, and fortreating microbial infections and conditions associated with suchinfections with the identified agonist or antagonist compounds. In astill further aspect, the invention relates to diagnostic assays fordetecting diseases associated with microbial infections and conditionsassociated with such infections, such as assays for detecting gidA1expression or activity.

[0008] Various changes and modifications within the spirit and scope ofthe disclosed invention will become readily apparent to those skilled inthe art from reading the following descriptions and from reading theother parts of the present disclosure.

DESCRIPTION OF THE INVENTION

[0009] The invention relates to gidA1 polypeptides and polynucleotidesas described in greater detail below. In particular, the inventionrelates to polypeptides and polynucleotides of a gidA1 of Streptococcuspneumoniae, which is related by amino acid sequence homology to gidApolypeptide. The invention relates especially to gidA1 having thenucleotide and amino acid sequences set out in Table 1 as SEQ ID NO: 1or 3 and SEQ ID NO: 2 or 4 respectively. TABLE 1 gidA1 Polynucleotideand Polypeptide Sequences (A) Streptococcus pneumoniae gidA1polynucleotide sequence [SEQ ID NO:1]. 5′-GAGGATATCCAGCTAGTTCCAGCCTTTTTAAAAACGGCCCTACCAGATTGGGAAGGCCAACTAAGACACATTCATCTTGAGGAATAGGAGAGAAACATGACTTATCATTTTACTGAAGAATACGATATTATTGTAATTGGTGCGGGACACGCTGGGGTTGAGGCTTCCTTGGCCGCTAGCCGTATGGGCTGTAAGGTCCTGCTTGCGACCATCAATATTGAAATGCTGGCTTTCATGCCTTGTAATCCCTCTATCGGTGGTTCTGCTAAGGGGATTGTCGTACGTGAAGTCGATGCCCTCGGTGGCGAGATGGCCAAGACCATTGACAAGACTTACATCCAGATGAAGATGCTCAACACAGGGAAGGGCCCAGCCGTTCGTGCCCTTCGTGCGCAGGCTGATAAGGAACTTTACTCTAAGGAAATGCGCAAGACAGTTGAAAATCAAGAAAATCTGACCCTTCGTCAAACCATGATTGATGAGATTTTGGTGGAAGATGGCAAGGTTGTCGGTGTGCGTACAGCCACCCATCAAGAATATGCTGCTAAGGCTGTTATTGTGACGACAGGGACTGCTCTCCGTGGGGAAATTATCATCGGAGACCTCAAGTACTCATCAGGTTCTAACCACAGCTTGGCTTCTATTAACCTAGCTGACAATCTCAAGGAACTGGGTCTCGAAATCGGTCGTTTCAAGACAGGAACCCCTCCACGTGTCAAGGCTTCTTCTATCAATTACGATGTGACGGAAATTCAGCCAGGAGACGAAGTGCCTAATCATTTCTCATACACTTCACGTGATGAGGATTATGTCAAAGATCAAGTGCCATGCTGGTTGACCTATACCAATGGTACCAGTCATGAGATTATCCAAAACAACCTCCACCGTGCGCCTATGTTTACAGGTGTGGTCAAGGGAGTGGGGCCTCGTTACTGTCCGTCGATTGAAGACAAGATTGTGCGCTTTGCGGACAAGGAACGTCACCAACTCTTCCTTGAGCCAGAAGGACGCAATACTGAGGAAGTCTATGTTCAAGGACTTTCAACCAGTCTGCCTGAGGATGTCCAGCGTGACTTGGTTCATTCCATCAAAGGTTTGGAAAATGCAGAGATGATGCGGACAGGTTATGCTATTGAGTATGATATGGTCTTGCCTCATCAGTTGCGTGCGACTTTGGAAACCAAGAAAATCTCAGGTCTCTTCACTGCTGGTCAGACAAATGGAACATCAGGTTATGAAGAAGCTGCTGGCCAAGGGATTATCGCGGGTATCAATGCGGCTCTGAAAATCCAAGGTAAACCTGAGTTGATTCTAAAACGAAGTGACGGTTATATCGGGGTGATGATCGACGACTTGGTGACCAAGGGAACCATTGAACCTTACCGTCTCTTGACCAGTCGTGCTGAATACCGTCTCATTCTTCGTCATGACAATGCTGATATGCGCTTGACTGAGATGGGACGCGAGATTGGCCTTGTGGATGATGAACGCTGGGCTCGTTTTGAAATCAAGAAAAATCAATTTGATAATGAGATGAAACGCCTAGACAGTATCAAACTCAAGCCAGTCAAGGAAACCAATGCTAAGGTTGAGGAAATGGGCTTCAAGCCGTTGACAGATGCGGTGACAGCCAAAGAATTCCTTCGCCGTCCAGAAGTTTCTTACCAAGATGTGGTGGCCTTCATCGGACCAGCTGCAGAAGACTTGGATGACAAGATTATCGAATTGATTGAAACAGAAATCAAGTACGAAGGCTATATTTCAAAAGCCATGGATCAGGTTGCCAAGATGAAACGTATGGAAGAAAAACGCATTCCAGCCAATATTGACTGGGATGACATCGATTCTATTGCGACGGAAGCTCGTCAGAAGTTCAAACTCATCAATCCAGAAACCATCGGCCAAGCCAGCCGTATTTCGGGAGTAAACCCAGCAGATATTTCTATTTTGATGGTGTATCTGGAAGGTAAAAATCGTAGTATTTCTAAAACTCTTCAAAAATCAAAATGATACGTCGTCGGCTTCTTACGAATGAGTTCAAAGCTTGGCTTTGATTCATCTCCAGCCTCCCATAGTTCCC CGAACTATGGGAGCTAACTC-3′ (B) Streptococcus pneumoniae gidA1polypeptide sequence deduced from a polynucleotide sequence in thistable [SEQ ID NO:2]. NH2-MTYHFTEEYDIIVIGAGHAGVEASLAASRMGCKVLLATINIEMLAFMPCNPSIGGSAKGIVVREVDALGGEMAKTIDKTYIQMKMLNTGKGPAVRALRAQADKELYSKEMRKTVENQENLTLRQTMIDEILVEDGKVVGVRTATHQEYAAKAVIVTTGTALRGEIIIGDLKYSSGSNHSLASINLADNLKELGLEIGRFKTGTPPRVKASSINYDVTEIQPGDEVPNHFSYTSRDEDYVKDQVPCWLTYTNGTSHEIIQNNLHRAPMFTGVVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGRNTEEVYVQGLSTSLPEDVQRDLVHSIKGLENAEMMRTGYAIEYDMVLPHQLRATLETKKISGLFTAGQTNGTSGYEEAAGQGIIAGINAALKIQGKPELILKRSDGYIGVMIDDLVTKGTIEPYRLLTSRAEYRLILRHDNADMRLTEMGREIGLVDDERWARFEIKKNQFDNEMKRLDSIKLKPVKETNAKVEEMGFKPLTDAVTAKEFLRRPEVSYQDVVAFIGPAAEDLDDKIIELIETEIKYEGYISKAMDQVAKMKRMEEKRIPANIDWDDIDSIATEARQKFKLINPETIGQASRISGVNPADISILMVYLEGKNRSISKTLQKSK-COOH (C) Streptococcus pneumoniae gidA1 ORP sequence [SEQ IDNO:3]. 5′-GGTGCGGGACACGCTGGGGTTGAGGCTTCCTTGGCCGCTAGCCGTATGGGCTGTAAGGTCCTGCTTGCGACCATCAATATTGAAATGCTGGCTTTCATGCCTTGTAATCCCTCTATCGGTGGTTCTGCTAAGGGGATTGTCGTACGTGAAGTCGATGCCCTCGGTGGCGAGATGGCCAAGACCATTGACAAGACTTACATCCAGATGAAGATGCTCAACACAGGGAAGGGCCCAGCCGTTCGTGCCCTTCGTGCGCAGGCTGATAAGGAACTTTACTCTAAGGAAATGCGCAAGACAGTTGAAAATCAAGAAAATCTGAGCCTTCGTCAAACCATGATTGATGAGATTTTGGTGGAAGATGGCAAGGTTGTCGGTGTGCGTACAGCCACCCATCAAGAATATGCTGCTAAGGCTGTTATTGTGACGACAGGGACTGCTCTCCGTGGGGAAATTATCATCGGAGACCTCAAGTACTCATCAGGTTCTAACCACAGCTTGGCTTCTATTAACCTAGCTGACAATCTCAAGGAACTGGGTCTCGAAATCGGTCGTTTCAAGACAGGAACCCCTCCACGTGTCAAGGCTTCTTCTATCAATTACGATGTGACGGAAATTCAGCCAGGAGACGAAGTGCCTAATCATTTCTCATACACTTCACGTGATGAGGATTATGTCAAAGATCAAGTGCCATGCTGGTTGACCTATACCAATGGTACCAGTCATGAGATTATCCAAAACAACCTCCACCGTGCGCCTATGTTTACAGGTGTGGTCAAGGGAGTGGGGCCTCGTTACTGTCCGTCGATTGAAGACAAGATTGTGCGCTTTGCGGACAAGGAACGTCACCAACTCTTCCTTGAGCCAGAAGGACGCAATACTGAGGAAGTCTATGTTCAAGGACTTTCAACCAGTCTGCCTGAGGATGTCCAGCGTGACTTGGTTCATTCCATCAAAGGTTTGGAAAATGCAGAGATGATGCGGACAGGTTATGCTATTGAGTATGATATGGTCTTGCCTCATCAGTTGCGTGCGACTTTGGAAACCAAGAAAATCTCAGGTCTCTTCACTGCTGGTCAGACAAATGGAACATCAGGTTATGAAGAAGCTGCTGGCCAAGGGATTATCGCGGGTATCAATGCGGCTCTGAAAATCCAAGGTAAACCTGAGTTGATTCTAAAACGAAGTGACGGTTATATCGGGGTGATGATCGACGACTTGGTGACCAAGGGAACCATTGAACCTTACCGTCTCTTGACCAGTCGTGCTGAATACCGTCTCATTCTTCGTCATGACAATGCTGATATGCGCTTGACTGAGATGGGACGCGAGATTGGCCTTGTGGATGATGAACGCTGGGCTCGTTTTGAAATCAAGAAAAATCAATTTGATAATGAGATGAAACGCCTAGACAGTATCAAACTCAAGCCAGTCAAGGAAACCAATGCTAAGGTTGAGGAAATGGGCTTCAAGCCGTTGACAGATGCGGTGACAGCCAAAGAATTCCTTCGCCGTCCAGAAGTTTCTTACCAAGATGTGGTGGCCTTCATCGGACCAGCTGCAGAAGACTTGGATGACAAGATTATCGAATTGATTGAAACAGAAATCAAGTACGAAGGGTATATTTCAAAAGCCATGGATCAGGTTGGCAAGATGAAACGTATGGAAGAAAAACGCATTCCAGCCAATATTGACTGGGATGACATCGATTCTATTGGGACGGAAGCTCGTCAGAAGTTCAAACTCATCAATCCAGAAACCATCGGGCAAGCCAGCCGTATTTCGGGAGTTAACCCAGCAGATATTTCTATTTTGATGGTGTATCTGGAAGGTAAAAATCGTA GTATTTCTAAAACTCCTCCAAAATCAAAATG-3′ (D) Streptococcus pneumoniaegidA1 polypeptide sequence deduced from a polynucleotide ORF sequence inthis table [SEQ ID NO:4]. NH2-GAGHAGVEASLAASRMGCKVLLATINIEMLAFMPCNPSIGGSAKGIVVREVDALGGEMAKTIDKTYIQMKMLNTGKGPAVRALRAQADKELYSKEMRKTVENQENLTLRQTMIDEILVEDGKVVGVRTATHQEYAAKAVIVTTGTALRGEIIIGDLKYSSGSNHSLASINLADNLKELGLEIGRFKTGTPPRVKASSINYDVTEIQPGDEVPNHFSYTSRDEDYVKDQVPCWLTYTNGTSHEIIQNNLHRAPMFTGVVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGRNTEEVYVQGLSTSLPEDVQRDLVHSIKGLENAEMMRTGYAIEYDMVLPHQLRATLETKKISGLFTAGQTNGTSGYEEAAGQGIIAGINAALKIQGKPELILKRSDGYIGVMIDDLVTKGTIEPYRLLTSRAEYRLILRHDNADMRLTEMGREIGLVDDERWARFEIKKNQFDNEMKRLDSIKLKPVKETNAKVEEMGFKPLTDAVTAKEFLRRPEVSYQDVVAFIGPAAEDLDDKIIELIETEIKYEGYISKAMDQVGKMKRMEEKRIPANIDWDDIDSIGTEARQKFKLINPETIGQASRISGVNPADISILMVYLEGKNRSISKTPPKSK-COOH

[0010] Deposited Materials

[0011] A deposit containing a Streptococcus pneumoniae 0100993 strainhas been deposited with the National Collections of Industrial and ManneBacteria Ltd. (herein “NCIMB”), 23 St. Machar Drive, Aberdeen AB2 1RY,Scotland on Apr. 11, 1996 and assigned deposit number 40794. The depositwas described as Streptococcus pneumoniae 0100993 on deposit. On Apr.17, 1996 a Streptococcus pneumoniae 0100993 DNA library in E. coli wassimilarly deposited with the NCIMB and assigned deposit number 40800.The Streptococcus pneumoniae strain deposit is referred to herein as“the deposited strain” or as “the DNA of the deposited strain.”

[0012] The deposited strain contains the full length gidA1 gene. Thesequence of the polynucleotides contained in the deposited strain, aswell as the amino acid sequence of any polypeptide encoded thereby, arecontrolling in the event of any conflict with any description ofsequences herein.

[0013] The deposit of the deposited strain has been made under the termsof the Budapest Treaty on the International Recognition of the Depositof Micro-organisms for Purposes of Patent Procedure. The strain will beirrevocably and without restriction or condition released to the publicupon the issuance of a patent. The deposited strain is provided merelyas convenience to those of skill in the art and is not an admission thata deposit is required for enablement, such as that required under 35U.S.C. §112.

[0014] A license may be required to make, use or sell the depositedstrain, and compounds derived therefrom, and no such license is herebygranted.

[0015] In one aspect of the invention there is provided an isolatednucleic acid molecule encoding a mature polypeptide expressible by theStreptococcus pneumoniae 0100993 strain, which polypeptide is containedin the deposited strain. Further provided by the invention are gidA1polynucleotide sequences in the deposited strain, such as DNA and RNA,and amino acid sequences encoded thereby. Also provided by the inventionare gidA1 polypeptide and polynucleotide sequences isolated from thedeposited strain.

[0016] Polypeptides

[0017] GidA1 polypeptide of the invention is substantiallyphylogenetically related to other proteins of the gidA family.

[0018] In one aspect of the invention there are provided polypeptides ofStreptococcus pneumoniae referred to herein as “gidA1” and “gidA1polypeptides” as well as biologically, diagnostically, prophylactically,clinically or therapeutically useful variants thereof, and compositionscomprising the same.

[0019] Among the particularly preferred embodiments of the invention arevariants of gidA1 polypeptide encoded by naturally occurring alleles ofthe gidA1 gene.

[0020] The present invention further provides for an isolatedpolypeptide which:

[0021] (a) comprises or consists of an amino acid sequence which has atleast 70% identity, preferably at least 80% identity, more preferably atleast 90% identity, yet more preferably at least 95% identity, mostpreferably at least 97-99% or exact identity, to that of SEQ ID NO:2over the entire length of SEQ ID NO:2;

[0022] (b) a polypeptide encoded by an isolated polynucleotidecomprising or consisting of a polynucleotide sequence which has at least70% identity, preferably at least 80% identity, more preferably at least90% identity, yet more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity to SEQ ID NO:1 over theentire length of SEQ ID NO:1;

[0023] (c) a polypeptide encoded by an isolated polynucleotidecomprising or consisting of a polynucleotide sequence encoding apolypeptide which has at least 70% identity, preferably at least 80%identity, more preferably at least 90% identity, yet more preferably atleast 95% identity, even more preferably at least 97-99% or exactidentity, to the amino acid sequence of SEQ ID NO:2, over the entirelength of SEQ ID NO:2; or

[0024] (d) a polypeptide encoded by an isolated polynucleotidecomprising or consisting of a polynucleotide sequence which has at least70% identity, preferably at least 80% identity, more preferably at least90% identity, yet more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity, to SEQ ID NO:1 over theentire length of SEQ ID NO:3;

[0025] (e) a polypeptide encoded by an isolated polynucleotidecomprising or consisting of a polynucleotide sequence which has at least70% identity, preferably at least 80% identity, more preferably at least90% identity, yet more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity to SEQ ID NO:3 over theentire length of SEQ ID NO:3; or

[0026] (f) a polypeptide encoded by an isolated polynucleotidecomprising or consisting of a polynucleotide sequence encoding apolypeptide which has at least 70% identity, preferably at least 80%identity, more preferably at least 90% identity, yet more preferably atleast 95% identity, even more preferably at least 97-99% or exactidentity, to the amino acid sequence of SEQ ID NO:4, over the entirelength of SEQ ID NO:4;

[0027] (g) comprises or consists of an amino acid sequence which has atleast 70% identity, preferably at least 80% identity, more preferably atleast 90% identity, yet more preferably at least 95% identity, mostpreferably at least 97-99% or exact identity, to the amino acid sequenceof SEQ ID NO:2 over the entire length of SEQ ID NO:4.

[0028] The polypeptides of the invention include a polypeptide of Table1 [SEQ ID NO:2 or 4] (in particular the mature polypeptide) as well aspolypeptides and fragments, particularly those which have the biologicalactivity of gidA1, and also those which have at least 70% identity to apolypeptide of Table 1 [SEQ ID NO:1 or 3]or the relevant portion,preferably at least 80% identity to a polypeptide of Table 1 [SEQ IDNO:2 or 4 and more preferably at least 90% identity to a polypeptide ofTable 1 [SEQ ID NO:2 or 4] and still more preferably at least 95%identity to a polypeptide of Table 1 [SEQ ID NO:2 or 4] and also includeportions of such polypeptides with such portion of the polypeptidegenerally containing at least 30 amino acids and more preferably atleast 50 amino acids.

[0029] The invention also includes a polypeptide consisting of orcomprising a polypeptide of the formula:

X-(R₁)_(m)-(R₂)-(R₃)_(n)-Y

[0030] wherein, at the amino terminus, X is hydrogen, a metal or anyother moiety described herein for modified polypeptides, and at thecarboxyl terminus, Y is hydrogen, a metal or any other moiety describedherein for modified polypeptides, R₁ and R₃ are any amino acid residueor modified amino acid residue, m is an integer between 1 and 1000 orzero, n is an integer between 1 and 1000 or zero, and R₂ is an aminoacid sequence of the invention, particularly an amino acid sequenceselected from Table 1 or modified forms thereof. In the formula above,R₂ is oriented so that its amino terminal amino acid residue is at theleft, covalently bound to R₁, and its carboxy terminal amino acidresidue is at the right, covalently bound to R₃. Any stretch of aminoacid residues denoted by either R₁ or R₃, where m and/or n is greaterthan 1, may be either a heteropolymer or a homopolymer, preferably aheteropolymer. Other preferred embodiments of the invention are providedwhere m is an integer between 1 and 50, 100 or 500, and n is an integerbetween 1 and 50, 100, or 500.

[0031] It is most preferred that a polypeptide of the invention isderived from Streptococcus pneumoniae, however, it may preferably beobtained from other organisms of the same taxonomic genus. A polypeptideof the invention may also be obtained, for example, from organisms ofthe same taxonomic family or order.

[0032] A fragment is a variant polypeptide having an amino acid sequencethat is entirely the same as part but not all of any amino acid sequenceof any polypeptide of the invention. As with gidA1 polypeptides,fragments may be “free-standing,” or comprised within a largerpolypeptide of which they form a part or region, most preferably as asingle continuous region in a single larger polypeptide.

[0033] Preferred fragments include, for example, truncation polypeptideshaving a portion of an amino acid sequence of Table 1 [SEQ ID NO:2 or4], or of variants thereof, such as a continuous series of residues thatincludes an amino- and/or carboxyl-terminal amino acid sequence.Degradation forms of the polypeptides of the invention produced by or ina host cell, particularly a Streptococcus pneumoniae, are alsopreferred. Further preferred are fragments characterized by structuralor functional attributes such as fragments that comprise alpha-helix andalpha-helix forming regions, beta-sheet and beta-sheet-forming regions,turn and turn-forming regions, coil and coil-forming regions,hydrophilic regions, hydrophobic regions, alpha amphipathic regions,beta amphipathic regions, flexible regions, surface-forming regions,substrate binding region, and high antigenic index regions.

[0034] Further preferred fragments include an isolated polypeptidecomprising an amino acid sequence having at least 15, 20, 30, 40, 50 or100 contiguous amino acids from the amino acid sequence of SEQ ID NO: 2,or an isolated polypeptide comprising an amino acid sequence having atleast 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated ordeleted from the amino acid sequence of SEQ ID NO: 2.

[0035] Also preferred are biologically active fragments which are thosefragments that mediate activities of gidA1, including those with asimilar activity or an improved activity, or with a decreasedundesirable activity. Also included are those fragments that areantigenic or immunogenic in an animal, especially in a human.Particularly preferred are fragments comprising receptors or domains ofenzymes that confer a function essential for viability of Streptococcuspneumoniae or the ability to initiate, or maintain cause Disease in anindividual, particularly a human.

[0036] Fragments of the polypeptides of the invention may be employedfor producing the corresponding full-length polypeptide by peptidesynthesis; therefore, these variants may be employed as intermediatesfor producing the full-length polypeptides of the invention. in additionto the standard single and triple letter representations for aminoacids, the term “X” or “Xaa” may also be used in describing certainpolypeptides of the invention. “X” and “Xaa” mean that any of the twentynaturally occurring amino acids may appear at such a designated positionin the polypeptide sequence.

[0037] Polynucleotides

[0038] It is an object of the invention to provide polynucleotides thatencode gidA1 polypeptides, particularly polynucleotides that encode thepolypeptide herein designated gidA1.

[0039] In a particularly preferred embodiment of the invention thepolynucleotide comprises a region encoding gidA1 polypeptides comprisinga sequence set out in Table 1 [SEQ ID NO:1 or 3] which includes a fulllength gene, or a variant thereof. The Applicants believe that this fulllength gene is essential to the growth and/or survival of an organismwhich possesses it, such as Streptococcus pneumoniae.

[0040] As a further aspect of the invention there are provided isolatednucleic acid molecules encoding and/or expressing gidA1 polypeptides andpolynucleotides, particularly Streptococcus pneumoniae gidA1polypeptides and polynucleotides, including, for example, unprocessedRNAs, ribozyme RNAs, mRNAs, cDNAs, genomic DNAs, B- and Z-DNAs. Furtherembodiments of the invention include biologically, diagnostically,prophylactically, clinically or therapeutically useful polynucleotidesand polypeptides, and variants thereof, and compositions comprising thesame.

[0041] Another aspect of the invention relates to isolatedpolynucleotides, including at least one full length gene, that encodes agidA1 polypeptide having a deduced amino acid sequence of Table 1 [SEQID NO:2 or 4] and polynucleotides closely related thereto and variantsthereof.

[0042] In another particularly preferred embodiment of the inventionthere is a gidA1 polypeptide from Streptococcus pneumoniae comprising orconsisting of an amino acid sequence of Table 1 [SEQ ID NO:2 or 4], or avariant thereof.

[0043] Using the information provided herein, such as a polynucleotidesequence set out in Table 1 [SEQ ID NO:1 or 3], a polynucleotide of theinvention encoding gidA1 polypeptide may be obtained using standardcloning and screening methods, such as those for cloning and sequencingchromosomal DNA fragments from bacteria using Streptococcus pneumoniae0100993 cells as starting material, followed by obtaining a full lengthclone. For example, to obtain a polynucleotide sequence of theinvention, such as a polynucleotide sequence given in Table 1 [SEQ IDNO:1 or 3], typically a library of clones of chromosomal DNA ofStreptococcus pneumoniae 0100993 in E. coli or some other suitable hostis probed with a radiolabeled oligonucleotide, preferably a 17-mer orlonger, derived from a partial sequence. Clones carrying DNA identicalto that of the probe can then be distinguished using stringenthybridization conditions. By sequencing the individual clones thusidentified by hybridization with sequencing primers designed from theoriginal polypeptide or polynucleotide sequence it is then possible toextend the polynucleotide sequence in both directions to determine afill length gene sequence. Conveniently, such sequencing is performed,for example, using denatured double stranded DNA prepared from a plasmidclone. Suitable techniques are described by Maniatis, T., Fritsch, E. F.and Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd Ed.;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).(see in particular Screening By Hybridization 1.90 and SequencingDenatured Double-Stranded DNA Templates 13.70). Direct genomic DNAsequencing may also be performed to obtain a full length gene sequence.Illustrative of the invention, each polynucleotide set out in Table 1[SEQ ID NO:1 or 3] was discovered in a DNA library derived fromStreptococcus pneumoniae 0100993.

[0044] Moreover, each DNA sequence set out in Table 1 [SEQ ID NO:1 or 3]contains an open reading frame encoding a protein having about thenumber of amino acid residues set forth in Table 1 [SEQ ID NO:2 or 4]with a deduced molecular weight that can be calculated using amino acidresidue molecular weight values well known to those skilled in the art.The polynucleotide of SEQ ID NO: 1, between nucleotide number 97 and thestop codon which begins at nucleotide number 2008 of SEQ ID NO:1,encodes the polypeptide of SEQ ID NO:2.

[0045] In a further aspect, the present invention provides for anisolated polynucleotide comprising or consisting of:

[0046] (a) a polynucleotide sequence which has at least 70% identity,preferably at least 80% identity, more preferably at least 90% identity,yet more preferably at least 95% identity, even more preferably at least97-99% or exact identity to SEQ ID NO:1 over the entire length of SEQ IDNO:1, or the entire length of SEQ ID NO:1 which encodes SEQ ID NO: 2;

[0047] (b) a polynucleotide sequence encoding a polypeptide which has atleast 70% identity, preferably at least 80% identity, more preferably atleast 90% identity, yet more preferably at least 95% identity, even morepreferably at least 97-99% or 100% exact, to the amino acid sequence ofSEQ ID NO:2, over the entire length of SEQ ID NO:2; or

[0048] (c) a nucleotide sequence which has at least 70% identity,preferably at least 80% identity, more preferably at least 90% identity,yet more preferably at least 95% identity, even more preferably at least97-99% or 100% identity, to SEQ ID NO:1 over the entire length of SEQ IDNO:3;

[0049] (d) a nucleotide sequence which has at least 70% identity,preferably at least 80% identity, more preferably at least 90% identity,yet more preferably at least 95% identity, even more preferably at least97-99% or exact identity to SEQ ID NO:3 over the entire length of SEQ IDNO:3; or

[0050] (e) a polynucleotide sequence encoding a polypeptide which has atleast 70% identity, preferably at least 80% identity, more preferably atleast 90% identity, yet more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity, to the amino acid sequenceof SEQ ID NO:4, over the entire length of SEQ ID NO:4.

[0051] A polynucleotide encoding a polypeptide of the present invention,including homologs and orthologs from species other than Streptococcuspneumoniae, may be obtained by a process which comprises the steps ofscreening an appropriate library under stringent hybridizationconditions with a labeled or detectable probe consisting of orcomprising the sequence of SEQ ID NO: 1 or 3 or a fragment thereof; andisolating a full-length gene and/or genomic clones containing saidpolynucleotide sequence.

[0052] The invention provides a polynucleotide sequence identical overits entire length to a coding sequence (open reading frame) in Table 1[SEQ ID NO:1 or 3]. Also provided by the invention is a coding sequencefor a mature polypeptide or a fragment thereof, by itself as well as acoding sequence for a mature polypeptide or a fragment in reading framewith another coding sequence, such as a sequence encoding a leader orsecretory sequence, a pre-, or pro- or prepro-protein sequence. Thepolynucleotide of the invention may also contain at least one non-codingsequence, including for example, but not limited to at least onenon-coding 5′ and 3′ sequence, such as the transcribed butnon-translated sequences, termination signals (such as rho-dependent andrho-independent termination signals), ribosome binding sites, Kozaksequences, sequences that stabilize mRNA, introns, and polyadenylationsignals. The polynucleotide sequence may also comprise additional codingsequence encoding additional amino acids. For example, a marker sequencethat facilitates purification of the fused polypeptide can be encoded.In certain embodiments of the invention, the marker sequence is ahexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) anddescribed in Gentz et al., Proc. Natl. Acad. Sci., USA 86: 821-824(1989), or an HA peptide tag (Wilson et al., Cell 37: 767 (1984), bothof which may be useful in purifying polypeptide sequence fused to them.Polynucleotides of the invention also include, but are not limited to,polynucleotides comprising a structural gene and its naturallyassociated sequences that control gene expression.

[0053] A preferred embodiment of the invention is a polynucleotide ofconsisting of or comprising nucleotide 97 to the nucleotide immediatelyupstream of or including nucleotide 2008 set forth in SEQ ID NO:1 ofTable 1, both of which encode the gidA1 polypeptide.

[0054] The invention also includes a polynucleotide consisting of orcomprising a polynucleotide of the formula:

X-(R₁)_(m)-(R₂)-(R₃)_(n)-Y

[0055] wherein, at the 5′ end of the molecule, X is hydrogen, a metal ora modified nucleotide residue, or together with Y defines a covalentbond, and at the 3′ end of the molecule, Y is hydrogen, a metal, or amodified nucleotide residue, or together with X defines the covalentbond, each occurrence of R₁ and R₃ is independently any nucleic acidresidue or modified nucleic acid residue, m is an integer between 1 and3000 or zero , n is an integer between 1 and 3000 or zero, and R₂ is anucleic acid sequence or modified nucleic acid sequence of theinvention, particularly a nucleic acid sequence selected from Table 1 ora modified nucleic acid sequence thereof. In the polynucleotide formulaabove, R₂ is oriented so that its 5′ end nucleic acid residue is at theleft, bound to R₁, and its 3′ end nucleic acid residue is at the right,bound to R₃. Any stretch of nucleic acid residues denoted by either R₁and/or R₂, where m and/or n is greater than 1, may be either aheteropolymer or a homopolymer, preferably a heteropolymer. Where, in apreferred embodiment, X and Y together define a covalent bond, thepolynucleotide of the above formula is a closed, circularpolynucleotide, which can be a double-stranded polynucleotide whereinthe formula shows a first strand to which the second strand iscomplementary. In another preferred embodiment m and/or n is an integerbetween 1 and 1000. Other preferred embodiments of the invention areprovided where m is an integer between 1 and 50, 100 or 500, and n is aninteger between 1 and 50, 100, or 500.

[0056] It is most preferred that a polynucleotide of the invention isderived from Streptococcus pneumoniae, however, it may preferably beobtained from other organisms of the same taxonomic genus. Apolynucleotide of the invention may also be obtained, for example, fromorganisms of the same taxonomic family or order.

[0057] The term “polynucleotide encoding a polypeptide” as used hereinencompasses polynucleotides that include a sequence encoding apolypeptide of the invention, particularly a bacterial polypeptide andmore particularly a polypeptide of the Streptococcus pneumoniae gidA1having an amino acid sequence set out in Table 1 [SEQ ID NO:2 or 4]. Theterm also encompasses polynucleotides that include a single continuousregion or discontinuous regions encoding the polypeptide (for example,polynucleotides interrupted by integrated phage, an integrated insertionsequence, an integrated vector sequence, an integrated transposonsequence, or due to RNA editing or genomic DNA reorganization) togetherwith additional regions, that also may contain coding and/or non-codingsequences.

[0058] The invention further relates to variants of the polynucleotidesdescribed herein that encode variants of a polypeptide having a deducedamino acid sequence of Table 1 [SEQ ID NO:2 or 4]. Fragments of apolynucleotides of the invention may be used, for example, to synthesizefull-length polynucleotides of the invention.

[0059] Further particularly preferred embodiments are polynucleotidesencoding gidA1 variants, that have the amino acid sequence of gidA1polypeptide of Table 1 [SEQ ID NO:2 or 4] in which several, a few, 5 to10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues are substituted,modified, deleted and/or added, in any combination. Especially preferredamong these are silent substitutions, additions and deletions, that donot alter the properties and activities of gidA1 polypeptide.

[0060] Further preferred embodiments of the invention arepolynucleotides that are at least 70% identical over their entire lengthto a polynucleotide encoding gidA1 polypeptide having an amino acidsequence set out in Table 1 [SEQ ID NO:2 or 4], and polynucleotides thatare complementary to such polynucleotides. Alternatively, most highlypreferred are polynucleotides that comprise a region that is at least80% identical over its entire length to a polynucleotide encoding gidA1polypeptide and polynucleotides complementary thereto. In this regard,polynucleotides at least 90% identical over their entire length to thesame are particularly preferred, and among these particularly preferredpolynucleotides, those with at least 95% are especially preferred.Furthermore, those with at least 97% are highly preferred among thosewith at least 95%, and among these those with at least 98% and at least99% are particularly highly preferred, with at least 99% being the morepreferred.

[0061] Preferred embodiments are polynucleotides encoding polypeptidesthat retain substantially the same biological function or activity asthe mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO:1 or 3].

[0062] In accordance with certain preferred embodiments of thisinvention there are provided polynucleotides that hybridize,particularly under stringent conditions, to gidA1 polynucleotidesequences, such as those polynucleotides in Table 1.

[0063] The invention further relates to polynucleotides that hybridizeto the polynucleotide sequences provided herein. In this regard, theinvention especially relates to polynucleotides that hybridize understringent conditions to the polynucleotides described herein. As hereinused, the terms “stringent conditions” and “stringent hybridizationconditions” mean hybridization occurring only if there is at least 95%and preferably at least 97% identity between the sequences. A specificexample of stringent hybridization conditions is overnight incubation at42° C. in a solution comprising: 50% formamide, 5× SSC (150 mM NaCl, 15mM trisodium citrate), 50 mM sodium phosphate pH7.6), 5× Denhardt'ssolution, 10% dextran sulfate, and 20 micrograms/ml of denatured,sheared salmon sperm DNA, followed by washing the hybridization supportin 0.1× SSC at about 65° C. Hybridization and wash conditions are wellknown and exemplified in Sambrook, et al., Molecular Cloning: ALaboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989),particularly Chapter 11 therein. Solution hybridization may also be usedwith the polynucleotide sequences provided by the invention.

[0064] The invention also provides a polynucleotide consisting of orcomprising a polynucleotide sequence obtained by screening anappropriate library containing the complete gene for a polynucleotidesequence set forth in SEQ ID NO:1 or 3 under stringent hybridizationconditions with a probe having the sequence of said polynucleotidesequence set forth in SEQ ID NO:1 or 3 or a fragment thereof, andisolating said polynucleotide sequence. Fragments useful for obtainingsuch a polynucleotide include, for example, probes and primers fullydescribed elsewhere herein.

[0065] As discussed elsewhere herein regarding polynucleotide assays ofthe invention, for instance, the polynucleotides of the invention, maybe used as a hybridization probe for RNA, cDNA and genomic DNA toisolate full-length cDNAs and genomic clones encoding gidA1 and toisolate cDNA and genomic clones of other genes that have a highidentity, particularly high sequence identity, to the gidA1 gene. Suchprobes generally will comprise at least 15 nucleotide residues or basepairs. Preferably, such probes will have at least 30 nucleotide residuesor base pairs and may have at least 50 nucleotide residues or basepairs. Particularly preferred probes will have at least 20 nucleotideresidues or base pairs and will have lee than 30 nucleotide residues orbase pairs.

[0066] A coding region of a gidA1 gene may be isolated by screeningusing a DNA sequence provided in Table 1 [SEQ ID NO: 1 or 3] tosynthesize an oligonucleotide probe. A labeled oligonucleotide having asequence complementary to that of a gene of the invention is then usedto screen a library of cDNA, genomic DNA or mRNA to determine whichmembers of the library the probe hybridizes to.

[0067] There are several methods available and well known to thoseskilled in the art to obtain full-length DNAs, or extend short DNAs, forexample those based on the method of Rapid Amplification of cDNA ends(RACE) (see, for example, Frohman, et al., PNAS USA 85: 8998-9002,1988). Recent modifications of the technique, exemplified by theMarathon™ technology (Clontech Laboratories Inc.) for example, havesignificantly simplified the search for longer cDNAs. In the Marathon™technology, cDNAs have been prepared from mRNA extracted from a chosentissue and an ‘adaptor’ sequence ligated onto each end. Nucleic acidamplification (PCR) is then carried out to amplify the “missing” 5′ endof the DNA using a combination of gene specific and adaptor specificoligonucleotide primers. The PCR reaction is then repeated using“nested” primers, that is, primers designed to anneal within theamplified product (typically an adaptor specific primer that annealsfurther 3′ in the adaptor sequence and a gene specific primer thatanneals further 5′ in the selected gene sequence). The products of thisreaction can then be analyzed by DNA sequencing and a full-length DNAconstructed either by joining the product directly to the existing DNAto give a complete sequence, or carrying out a separate full-length PCRusing the new sequence information for the design of the 5′ primer.

[0068] The polynucleotides and polypeptides of the invention may beemployed, for example, as research reagents and materials for discoveryof treatments of and diagnostics for diseases, particularly humandiseases, as further discussed herein relating to polynucleotide assays.

[0069] The polynucleotides of the invention that are oligonucleotidesderived from a sequence of Table 1 [SEQ ID NOS:1 or 2 or 3 or 4] may beused in the processes herein as described, but preferably for PCR, todetermine whether or not the polynucleotides identified herein in wholeor in part are transcribed in bacteria in infected tissue. It isrecognized that such sequences will also have utility in diagnosis ofthe stage of infection and type of infection the pathogen has attained.

[0070] The invention also provides polynucleotides that encode apolypeptide that is the mature protein plus additional amino orcarboxyl-terminal amino acids, or amino acids interior to the maturepolypeptide (when the mature form has more than one polypeptide chain,for instance). Such sequences may play a role in processing of a proteinfrom precursor to a mature form, may allow protein transport, maylengthen or shorten protein half-life or may facilitate manipulation ofa protein for assay or production, among other things. As generally isthe case in vivo, the additional amino acids may be processed away fromthe mature protein by cellular enzymes.

[0071] For each and every polynucleotide of the invention there isprovided a polynucleotide complementary to it. It is preferred thatthese complementary polynucleotides are fully complementary to eachpolynucleotide with which they are complementary.

[0072] A precursor protein, having a mature form of the polypeptidefused to one or more prosequences may be an inactive form of thepolypeptide. When prosequences are removed such inactive precursorsgenerally are activated. Some or all of the prosequences may be removedbefore activation. Generally, such precursors are called proproteins.

[0073] In addition to the standard A, G, C, T/U representations fornucleotides, the term “N” may also be used in describing certainpolynucleotides of the invention. “N” means that any of the four DNA orRNA nucleotides may appear at such a designated position in the DNA orRNA sequence, except it is preferred that N is not a nucleic acid thatwhen taken in combination with adjacent nucleotide positions, when readin the correct reading frame, would have the effect of generating apremature termination codon in such reading frame.

[0074] In sum, a polynucleotide of the invention may encode a matureprotein, a mature protein plus a leader sequence (which may be referredto as a preprotein), a precursor of a mature protein having one or moreprosequences that are not the leader sequences of a preprotein, or apreproprotein, which is a precursor to a proprotein, having a leadersequence and one or more prosequences, which generally are removedduring processing steps that produce active and mature forms of thepolypeptide.

[0075] Vectors, Host Cells, Expression Systems

[0076] The invention also relates to vectors that comprise apolynucleotide or polynucleotides of the invention, host cells that aregenetically engineered with vectors of the invention and the productionof polypeptides of the invention by recombinant techniques. Cell-freetranslation systems can also be employed to produce such proteins usingRNAs derived from the DNA constructs of the invention.

[0077] Recombinant polypeptides of the present invention may be preparedby processes well known in those skilled in the art from geneticallyengineered host cells comprising expression systems. Accordingly, in afurther aspect, the present invention relates to expression systemswhich comprise a polynucleotide or polynucleotides of the presentinvention, to host cells which are genetically engineered with suchexpression systems, and to the production of polypeptides of theinvention by recombinant techniques.

[0078] For recombinant production of the polypeptides of the invention,host cells can be genetically engineered to incorporate expressionsystems or portions thereof or polynucleotides of the invention.Introduction of a polynucleotide into the host cell can be effected bymethods described in many standard laboratory manuals, such as Davis, etal., BASIC METHODS INMOLECULAR BIOLOGY, (1986) and Sambrook, et al.,MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calciumphosphate transfection, DEAE-dextran mediated transfection,transvection, microinjection, cationic lipid-mediated transfection,electroporation, transduction, scrape loading, ballistic introductionand infection.

[0079] Representative examples of appropriate hosts include bacterialcells, such as cells of streptococci, staphylococci, enterococci E.coli, streptomyces, cyanobacteria, Bacillus subtilis, and Streptococcuspneumoniae; fungal cells, such as cells of a yeast, Kluveromyces,Saccharomyces, a basidiomycete, Candida albicans and Aspergillus; insectcells such as cells of Drosophila S2 and Spodoptera Sf9; animal cellssuch as CHO, COS, HeLa, C127, 3T3, BHK, 293, CV-1 and Bowes melanomacells; and plant cells, such as cells of a gymnosperm or angiosperm.

[0080] A great variety of expression systems can be used to produce thepolypeptides of the invention. Such vectors include, among others,chromosomal-, episomal- and virus-derived vectors, for example, vectorsderived from bacterial plasmids, from bacteriophage, from transposons,from yeast episomes, from insertion elements, from yeast chromosomalelements, from viruses such as baculoviruses, papova viruses, such asSV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabiesviruses, picomaviruses and retroviruses, and vectors derived fromcombinations thereof, such as those derived from plasmid andbacteriophage genetic elements, such as cosmids and phagemids. Theexpression system constructs may contain control regions that regulateas well as engender expression. Generally, any system or vector suitableto maintain, propagate or express polynucleotides and/or to express apolypeptide in a host may be used for expression in this regard. Theappropriate DNA sequence may be inserted into the expression system byany of a variety of well-known and routine techniques, such as, forexample, those set forth in Sambrook et al., MOLECULAR CLONING, ALABORATORY MANUAL, (supra).

[0081] In recombinant expression systems in eukaryotes, for secretion ofa translated protein into the lumen of the endoplasmic reticulum, intothe periplasmic space or into the extracellular environment, appropriatesecretion signals may be incorporated into the expressed polypeptide.These signals may be endogenous to the polypeptide or they may beheterologous signals.

[0082] Polypeptides of the invention can be recovered and purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxyladatitechromatography, and lectin chromatography. Most preferably, highperformance liquid chromatography is employed for purification. Wellknown techniques for refolding protein may be employed to regenerateactive conformation when the polypeptide is denatured during isolationand or purification.

[0083] Diagnostic, Prognostic, Serotyping and Mutation Assays

[0084] This invention is also related to the use of gidA1polynucleotides and polypeptides of the invention for use as diagnosticreagents. Detection of gidA1 polynucleotides and/or polypeptides in aeukaryote, particularly a mammal, and especially a human, will provide adiagnostic method for diagnosis of disease, staging of disease orresponse of an infectious organism to drugs. Eukaryotes, particularlymammals, and especially humans, particularly those infected or suspectedto be infected with an organism comprising the gidA1 gene or protein,may be detected at the nucleic acid or amino acid level by a variety ofwell known techniques as well as by methods provided herein.

[0085] Polypeptides and polynucleotides for prognosis, diagnosis orother analysis may be obtained from a putatively infected and/orinfected individual's bodily materials. Polynucleotides from any ofthese sources, particularly DNA or RNA, may be used directly fordetection or may be amplified enzymatically by using PCR or any otheramplification technique prior to analysis. RNA, particularly mRNA, cDNAand genomic DNA may also be used in the same ways. Using amplification,characterization of the species and strain of infectious or residentorganism present in an individual, may be made by an analysis of thegenotype of a selected polynucleotide of the organism. Deletions andinsertions can be detected by a change in size of the amplified productin comparison to a genotype of a reference sequence selected from arelated organism, preferably a different species of the same genus or adifferent strain of the same species. Point mutations can be identifiedby hybridizing amplified DNA to labeled gidA1 polynucleotide sequences.Perfectly or significantly matched sequences can be distinguished fromimperfectly or more significantly mismatched duplexes by DNase or RNasedigestion, for DNA or RNA respectively, or by detecting differences inmelting temperatures or renaturation kinetics. Polynucleotide sequencedifferences may also be detected by alterations in the electrophoreticmobility of polynucleotide fragments in gels as compared to a referencesequence. This may be carried out with or without denaturing agents.Polynucleotide differences may also be detected by direct DNA or RNAsequencing. See, for example, Myers et al., Science, 230: 1242 (1985).Sequence changes at specific locations also may be revealed by nucleaseprotection assays, such as RNase, V1 and S1 protection assay or achemical cleavage method. See, for example, Cotton et al., Proc. Natl.Acad. Sci., USA. 85: 4397-4401 (1985).

[0086] In another embodiment, an array of oligonucleotides probescomprising gidA1 nucleotide sequence or fragments thereof can beconstructed to conduct efficient screening of, for example, geneticmutations, serotype, taxonomic classification or identification. Arraytechnology methods are well known and have general applicability and canbe used to address a variety of questions in molecular geneticsincluding gene expression, genetic linkage, and genetic variability(see, for example, Chee et al., Science, 274: 610 (1996)).

[0087] Thus in another aspect, the present invention relates to adiagnostic kit which comprises:

[0088] (a) a polynucleotide of the present invention, preferably thenucleotide sequence of SEQ ID NO:1 or 3, or a fragment thereof;

[0089] (b) a nucleotide sequence complementary to that of (a); (c) apolypeptide of the present invention, preferably the polypeptide of SEQID NO:2 or 4 or a fragment thereof, or

[0090] (d) an antibody to a polypeptide of the present invention,preferably to the polypeptide of SEQ ID NO:2 or 4.

[0091] It will be appreciated that in any such kit, (a), (b), (c) or (d)may comprise a substantial component. Such a kit will be of use indiagnosing a disease or susceptibility to a Disease, among others.

[0092] This invention also relates to the use of polynucleotides of thepresent invention as diagnostic reagents. Detection of a mutated form ofa polynucleotide of the invention, preferable, SEQ ID NO:1 or 3 which isassociated with a disease or pathogenicity will provide a diagnostictool that can add to, or define, a diagnosis of a disease, a prognosisof a course of disease, a determination of a stage of disease, or asusceptibility to a disease, which results from under-expression,over-expression or altered expression of the polynucleotide. Organisms,particularly infectious organisms, carrying mutations in suchpolynucleotide may be detected at the polynucleotide level by a varietyof techniques, such as those described elsewhere herein.

[0093] The nucleotide sequences of the present invention are alsovaluable for organism chromosome identification. The sequence isspecifically targeted to, and can hybridize with, a particular locationon an organism's chromosome, particularly to a Streptococcus pneumoniaechromosome. The mapping of relevant sequences to chromosomes accordingto the present invention may be an important step in correlating thosesequences with pathogenic potential and/or an ecological niche of anorganism and/or drug resistance of an organism, as well as theessentiality of the gene to the organism. Once a sequence has beenmapped to a precise chromosomal location, the physical position of thesequence on the chromosome can be correlated with genetic map data. Suchdata may be found on-line in a sequence database. The relationshipbetween genes and diseases that have been mapped to the same chromosomalregion are then identified through known genetic methods, for example,through linkage analysis (coinheritance of physically adjacent genes) ormating studies, such as by conjugation.

[0094] The differences in a polynucleotide and/or polypeptide sequencebetween organisms possessing a first phenotype and organisms possessinga different, second different phenotype can also be determined. If amutation is observed in some or all organisms possessing the firstphenotype but not in any organisms possessing the second phenotype, thenthe mutation is likely to be the causative agent of the first phenotype.

[0095] Cells from an organism carrying mutations or polymorphisms(allelic variations) in a polynucleotide and/or polypeptide of theinvention may also be detected at the polynucleotide or polypeptidelevel by a variety of techniques, to allow for serotyping, for example.For example, RT-PCR can be used to detect mutations in the RNA. It isparticularly preferred to use RT-PCR in conjunction with automateddetection systems, such as, for example, GeneScan. RNA, cDNA or genomicDNA may also be used for the same purpose, PCR. As an example, PCRprimers complementary to a polynucleotide encoding gidA1 polypeptide canbe used to identify and analyze mutations. Examples of representativeprimers are shown below in Table 2. TABLE 2 Primers for amplification ofgidA1 polynucleotides SEQ ID NO PRIMER SEQUENCE 55′-ATGACTTATCATTTTACTGA-3′ 6 5′-TCATTTTGATTTTTGAAGAG-3′

[0096] The invention also includes primers of the formula:

X-(R₁)_(m)-(R₂)-(R₃)_(n)-Y

[0097] wherein, at the 5′ end of the molecule, X is hydrogen, a metal ora modified nucleotide residue, and at the 3′ end of the molecule, Y ishydrogen, a metal or a modified nucleotide residue, R₁ and R₃ are anynucleic acid residue or modified nucleotide residue, m is an integerbetween 1 and 20 or zero , n is an integer between 1 and 20 or zero, andR₂ is a primer sequence of the invention, particularly a primer sequenceselected from Table 2. In the polynucleotide formula above R₂ isoriented so that its 5′ end nucleotide residue is at the left, bound toR₁ and its 3′ end nucleotide residue is at the right, bound to R₃. Anystretch of nucleic acid residues denoted by either R group, where mand/or n is greater than 1, may be either a heteropolymer or ahomopolymer, preferably a heteropolymer being complementary to a regionof a polynucleotide of Table 1. In a preferred embodiment m and/or n isan integer between 1 and 10.

[0098] The invention further provides these primers with 1, 2, 3 or 4nucleotides removed from the 5′ and/or the 3′ end. These primers may beused for, among other things, amplifying gidA1 DNA and/or RNA isolatedfrom a sample derived from an individual, such as a bodily material. Theprimers may be used to amplify a polynucleotide isolated from aninfected individual, such that the polynucleotide may then be subject tovarious techniques for elucidation of the polynucleotide sequence. Inthis way, mutations in the polynucleotide sequence may be detected andused to diagnose and/or prognose the infection or its stage or course,or to serotype and/or classify the infectious agent.

[0099] The invention further provides a process for diagnosing, disease,preferably bacterial infections, more preferably infections caused byStreptococcus pneumoniae, comprising determining from a sample derivedfrom an individual, such as a bodily material, an increased level ofexpression of polynucleotide having a sequence of Table 1 [SEQ ID NO: 1or 3]. Increased or decreased expression of a gidA1 polynucleotide canbe measured using any on of the methods well known in the art for thequantitation of polynucleotides, such as, for example, amplification,PCR, RT-PCR, RNase protection, Northern blotting, spectrometry and otherhybridization methods.

[0100] In addition, a diagnostic assay in accordance with the inventionfor detecting over-expression of gidA1 polypeptide compared to normalcontrol tissue samples may be used to detect the presence of aninfection, for example. Assay techniques that can be used to determinelevels of a gidA1 polypeptide, in a sample derived from a host, such asa bodily material, are well-known to those of skill in the art. Suchassay methods include radioimmunoassays, competitive-binding assays,Western Blot analysis, antibody sandwich assays, antibody detection andELISA assays.

[0101] Differential Expression

[0102] The polynucleotides and polynucleotides of the invention may beused as reagents for differential screening methods. There are manydifferential screening and differential display methods known in the artin which the polynucleotides and polypeptides of the invention may beused. For example, the differential display technique is described byChuang et al., J. Bacteriol. 175:2026-2036 (1993). This methodidentifies those genes which are expressed in an organism by identifyingmRNA present using randomly-primed RT-PCR. By comparing pre-infectionand post infection profiles, genes up and down regulated duringinfection can be identified and the RT-PCR product sequenced and matchedto ORF “unknowns.”

[0103] In Vivo Expression Technology (IVET) is described by Camilli etal., Proc. Nat'l. Acad. Sci. USA. 91:2634-2638 (1994). IVET identifiesgenes up-regulated during infection when compared to laboratorycultivation, implying an important role in infection. ORFs identified bythis technique are implied to have a significant role in infectionestablishment and/or maintenance. In this technique random chromosomalfragments of target organism are cloned upstream of a promoter-lessrecombinase gene in a plasmid vector. This construct is introduced intothe target organism which carries an antibiotic resistance gene flankedby resolvase sites. Growth in the presence of the antibiotic removesfrom the population those fragments cloned into the plasmid vectorcapable of supporting transcription of the recombinase gene andtherefore have caused loss of antibiotic resistance. The resistant poolis introduced into a host and at various times after infection bacteriamay be recovered and assessed for the presence of antibiotic resistance.The chromosomal fragment carried by each antibiotic sensitive bacteriumshould carry a promoter or portion of a gene normally upregulated duringinfection. Sequencing upstream of the recombinase gene allowsidentification of the up regulated gene.

[0104] RT-PCR may also be used to analyze gene expression patterns. ForRT PCR using the polynucleotides of the invention, messenger RNA isisolated from bacterial infected tissue, e.g., 48 hour murine lunginfections, and the amount of each mRNA species assessed by reversetranscription of the RNA sample primed with random hexanucleotidesfollowed by PCR with gene specific primer pairs. The determination ofthe presence and amount of a particular mRNA species by quantificationof the resultant PCR product provides information on the bacterial geneswhich are transcribed in the infected tissue. Analysis of genetranscription can be carried out at different times of infection to gaina detailed knowledge of gene regulation in bacterial pathogenesisallowing for a clearer understanding of which gene products representtargets for screens for antibacterials. Because of the gene specificnature of the PCR primers employed it should be understood that thebacterial mRNA preparation need not be free of mammalian RNA. Thisallows the investigator to carry out a simple and quick RNA preparationfrom infected tissue to obtain bacterial mRNA species which are veryshort lived in the bacterium (in the order of 2 minute halflives).Optimally the bacterial mRNA is prepared from infected murine lungtissue by mechanical disruption in the presence of TRIzole (GIBCO-BRL)for very short periods of time, subsequent processing according to themanufacturers of TRIzole reagent and DNAase treatment to removecontaminating DNA. Preferably the process is optimized by finding thoseconditions which give a maximum amount of Streptococcus pneumoniae 16Sribosomal RNA as detected by probing Northerns with a suitably labeledsequence specific oligonucleotide probe. Typically a 5′ dye labeledprimer is used in each PCR primer pair in a PCR reaction which isterminated optimally between 8 and 25 cycles. The PCR products areseparated on 6% polyacrylamide gels with detection and quantificationusing GeneScanner (manufactured by ABI).

[0105] Gridding and Polynucleotide Subtraction

[0106] Methods have been described for obtaining information about geneexpression and identity using so called “high density DNA arrays” orgrids. See, e.g., M. Chee et al., Science, 274:610-614 (1996) and otherreferences cited therein. Such gridding assays have been employed toidentify certain novel gene sequences, referred to as Expressed SequenceTags (EST) (Adams et a., Science, 252:1651-1656 (1991)). A variety oftechniques have also been described for identifying particular genesequences on the basis of their gene products. For example, seeInternational Patent Application No. WO91/07087, published May 30, 1991.In addition, methods have been described for the amplification ofdesired sequences. For example, see International Patent Application No.WO91/17271, published Nov. 14, 1991.

[0107] The polynucleotides of the invention may be used as components ofpolynucleotide arrays, preferably high density arrays or grids. Thesehigh density arrays are particularly useful for diagnostic andprognostic purposes. For example, a set of spots each comprising adifferent gene, and further comprising a polynucleotide orpolynucleotides of the invention, may be used for probing, such as usinghybridization or nucleic acid amplification, using a probes obtained orderived from a bodily sample, to determine the presence of a particularpolynucleotide sequence or related sequence in an individual. Such apresence may indicate the presence of a pathogen, particularlyStreptococcus pneumoniae, and may be useful in diagnosing and/orprognosing disease or a course of disease. A grid comprising a number ofvariants of the polynucleotide sequence of SEQ ID NO:1 or 3 arepreferred. Also preferred is a comprising a number of variants of apolynucleotide sequence encoding the polypeptide sequence of SEQ ID NO:2or 4.

[0108] Antibodies

[0109] The polypeptides and polynucleotides of the invention or variantsthereof, or cells expressing the same can be used as immunogens toproduce antibodies immunospecific for such polypeptides orpolynucleotides respectively.

[0110] In certain preferred embodiments of the invention there areprovided antibodies against gidA1 polypeptides or polynucleotides.

[0111] Antibodies generated against the polypeptides or polynucleotidesof the invention can be obtained by administering the polypeptidesand/or polynucleotides of the invention, or epitope-bearing fragments ofeither or both, analogues of either or both, or cells expressing eitheror both, to an animal, preferably a nonhuman, using routine protocols.For preparation of monoclonal antibodies, any technique known in the artthat provides antibodies produced by continuous cell line cultures canbe used. Examples include various techniques, such as those in Kohler,G. and Milstein, C., Nature 256: 495-497 (1975); Kozbor et al.,Immunology Today 4: 72 (1983); Cole et al., pg. 77-96 in MONOCLONALANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).

[0112] Techniques for the production of single chain antibodies (U.S.Pat. No. 4,946,778) can be adapted to produce single chain antibodies topolypeptides or polynucleotides of this invention. Also, transgenicmice, or other organisms such as other mammals, may be used to expresshumanized antibodies immunospecific to the polypeptides orpolynucleotides of the invention.

[0113] Alternatively, phage display technology may be utilized to selectantibody genes with binding activities towards a polypeptide of theinvention either from repertoires of PCR amplified v-genes oflymphocytes from humans screened for possessing anti-gidA1 or from naivelibraries (McCafferty, et al., (1990), Nature 348, 552-554; Marks, etal., (1992) Biotechnology 10, 779-783). The affinity of these antibodiescan also be improved by, for example, chain shuffling (Clackson et al.,(1991) Nature 352: 628).

[0114] The above-described antibodies may be employed to isolate or toidentify clones expressing the polypeptides or polynucleotides of theinvention to purify the polypeptides or polynucleotides by, for example,affinity chromatography.

[0115] Thus, among others, antibodies against gidA1-polypeptide orgidA1-polynucleotide may be employed to treat infections, particularlybacterial infections.

[0116] Polypeptide variants include antigenically, epitopically orimmunologically equivalent variants form a particular aspect of thisinvention.

[0117] A polypeptide or polynucleotide of the invention, such as anantigenically or immunologically equivalent derivative or a fusionprotein of the polypeptide is used as an antigen to immunize a mouse orother animal such as a rat or chicken. The fusion protein may providestability to the polypeptide. The antigen may be associated, for exampleby conjugation, with an immunogenic carrier protein for example bovineserum albumin, keyhole limpet haemocyanin or tetanus toxoid.Alternatively, a multiple antigenic polypeptide comprising multiplecopies of the polypeptide, or an antigenically or immunologicallyequivalent polypeptide thereof may be sufficiently antigenic to improveimmunogenicity so as to obviate the use of a carrier.

[0118] Preferably, the antibody or variant thereof is modified to makeit less immunogenic in the individual. For example, if the individual ishuman the antibody may most preferably be “humanized,” where thecomplimentarity determining region or regions of the hybridoma-derivedantibody has been transplanted into a human monoclonal antibody, forexample as described in Jones et al. (1986), Nature 321, 522-525 orTempest et al., (1991) Biotechnology 9, 266-273.

[0119] In accordance with an aspect of the invention, there is providedthe use of a polynucleotide of the invention for therapeutic orprophylactic purposes, in particular genetic immunization. Among theparticularly preferred embodiments of the invention are naturallyoccurring allelic variants of gidA1 polynucleotides and polypeptidesencoded thereby.

[0120] The use of a polynucleotide of the invention in geneticimmunization will preferably employ a suitable delivery method such asdirect injection of plasmid DNA into muscles (Wolff et al., Hum MolGenet (1992) 1: 363, Manthorpe et al., Hum. Gene Ther. (1983) 4: 419),delivery of DNA complexed with specific protein carriers (Wu et al., JBiol Chem. (1989) 264: 16985), coprecipitation of DNA with calciumphosphate (Benvenisty & Reshef, PNAS USA, (1986) 83: 9551),encapsulation of DNA in various forms of liposomes (Kaneda et al.,Science (1989) 243: 375), particle bombardment (Tang et al., Nature(1992) 356:152, Eisenbraun et al., DNA Cell Biol (1993) 12: 791) and invivo infection using cloned retroviral vectors (Seeger et al., PNAS USA(1984) 81: 5849).

[0121] Antagonists and Agonists—Assays and Molecules

[0122] Polypeptides and polynucleotides of the invention may also beused to assess the binding of small molecule substrates and ligands in,for example, cells, cell-free preparations, chemical libraries, andnatural product mixtures. These substrates and ligands may be naturalsubstrates and ligands or may be structural or functional mimetics. See,e.g., Coligan et al., Current Protocols in Immunology 1(2): Chapter 5(1991).

[0123] Polypeptides and polynucleotides of the present invention areresponsible for many biological functions, including many diseasestates, in particular the Diseases hereinbefore mentioned. It istherefore desirable to devise screening methods to identify compoundswhich stimulate or which inhibit the function of the polypeptide orpolynucleotide. Accordingly, in a further aspect, the present inventionprovides for a method of screening compounds to identify those whichstimulate or which inhibit the function of a polypeptide orpolynucleotide of the invention, as well as related polypeptides andpolynucleotides. In general, agonists or antagonists may be employed fortherapeutic and prophylactic purposes for such Diseases as hereinbeforementioned. Compounds may be identified from a variety of sources, forexample, cells, cell-free preparations, chemical libraries, and naturalproduct mixtures. Such agonists, antagonists or inhibitors so-identifiedmay be natural or modified substrates, ligands, receptors, enzymes,etc., as the case may be, of gidA1 polypeptides and polynucleotides; ormay be structural or functional mimetics thereof (see Coligan et al.,Current Protocols in Immunology 1(2):Chapter 5 (1991)).

[0124] The screening methods may simply measure the binding of acandidate compound to the polypeptide or polynucleotide, or to cells ormembranes bearing the polypeptide or polynucleotide, or a fusion proteinof the polypeptide by means of a label directly or indirectly associatedwith the candidate compound. Alternatively, the screening method mayinvolve competition with a labeled competitor. Further, these screeningmethods may test whether the candidate compound results in a signalgenerated by activation or inhibition of the polypeptide orpolynucleotide, using detection systems appropriate to the cellscomprising the polypeptide or polynucleotide. Inhibitors of activationare generally assayed in the presence of a known agonist and the effecton activation by the agonist by the presence of the candidate compoundis observed. Constitutively active polypeptide and/or constitutivelyexpressed polypeptides and polynucleotides may be employed in screeningmethods for inverse agonists or inhibitors, in the absence of an agonistor inhibitor, by testing whether the candidate compound results ininhibition of activation of the polypeptide or polynucleotide, as thecase may be. Further, the screening methods may simply comprise thesteps of mixing a candidate compound with a solution containing apolypeptide or polynucleotide of the present invention, to form amixture, measuring gidA1 polypeptide and/or polynucleotide activity inthe mixture, and comparing the gidA1 polypeptide and/or polynucleotideactivity of the mixture to a standard. Fusion proteins, such as thosemade from Fc portion and gidA1 polypeptide, as hereinbefore described,can also be used for high-throughput screening assays to identifyantagonists of the polypeptide of the present invention, as well as ofphylogenetically and and/or functionally related polypeptides (see D.Bennett et al., J Mol Recognition, 8:52-58 (1995); and K. Johanson etal., J Biol Chem, 270(16):9459-9471 (1995)).

[0125] The polynucleotides, polypeptides and antibodies that bind toand/or interact with a polypeptide of the present invention may also beused to configure screening methods for detecting the effect of addedcompounds on the production of mRNA and/or polypeptide in cells. Forexample, an ELISA assay may be constructed for measuring secreted orcell associated levels of polypeptide using monoclonal and polyclonalantibodies by standard methods known in the art. This can be used todiscover agents which may inhibit or enhance the production ofpolypeptide (also called antagonist or agonist, respectively) fromsuitably manipulated cells or tissues.

[0126] The invention also provides a method of screening compounds toidentify those which enhance (agonist) or block (antagonist) the actionof gidA1 polypeptides or polynucleotides, particularly those compoundsthat are bacteristatic and/or bactericidal. The method of screening mayinvolve high-throughput techniques. For example, to screen for agonistsor antagonists, a synthetic reaction mix, a cellular compartment, suchas a membrane, cell envelope or cell wall, or a preparation of anythereof, comprising gidA1 polypeptide and a labeled substrate or ligandof such polypeptide is incubated in the absence or the presence of acandidate molecule that may be a gidA1 agonist or antagonist. Theability of the candidate molecule to agonize or antagonize the gidA1polypeptide is reflected in decreased binding of the labeled ligand ordecreased production of product from such substrate. Molecules that bindgratuitously, i.e., without inducing the effects of gidA1 polypeptideare most likely to be good antagonists. Molecules that bind well and, asthe case may be, increase the rate of product production from substrate,increase signal transduction, or increase chemical channel activity areagonists. Detection of the rate or level of, as the case may be,production of product from substrate, signal transduction, or chemicalchannel activity may be enhanced by using a reporter system. Reportersystems that may be useful in this regard include but are not limited tocalorimetric, labeled substrate converted into product, a reporter genethat is responsive to changes in gidA1 polynucleotide or polypeptideactivity, and binding assays known in the art.

[0127] Polypeptides of the invention may be used to identify membranebound or soluble receptors, if any, for such polypeptide, throughstandard receptor binding techniques known in the art. These techniquesinclude, but are not limited to, ligand binding and crosslinking assaysin which the polypeptide is labeled with a radioactive isotope (forinstance, ¹²⁵I), chemically modified (for instance, biotinylated), orfused to a peptide sequence suitable for detection or purification, andincubated with a source of the putative receptor (e.g., cells, cellmembranes, cell supernatants, tissue extracts, bodily materials). Othermethods include biophysical techniques such as surface plasmon resonanceand spectroscopy. These screening methods may also be used to identifyagonists and antagonists of the polypeptide which compete with thebinding of the polypeptide to its receptor(s), if any. Standard methodsfor conducting such assays are well understood in the art.

[0128] The fluorescence polarization value for a fluorescently-taggedmolecule depends on the rotational correlation time or tumbling rate.Protein complexes, such as formed by gidA1 polypeptide associating withanother gidA1 polypeptide or other polypeptide, labeled to comprise afluorescently-labeled molecule will have higher polarization values thana fluorescently labeled monomeric protein. It is preferred that thismethod be used to characterize small molecules that disrupt polypeptidecomplexes.

[0129] Fluorescence energy transfer may also be used characterize smallmolecules that interfere with the formation of gidA1 polypeptide dimers,trimers, tetramers or higher order structures, or structures formed bygidA1 polypeptide bound to another polypeptide. GidA1 polypeptide can belabeled with both a donor and acceptor fluorophore. Upon mixing of thetwo labeled species and excitation of the donor fluorophore,fluorescence energy transfer can be detected by observing fluorescenceof the acceptor. Compounds that block dimerization will inhibitfluorescence energy transfer.

[0130] Surface plasmon resonance can be used to monitor the effect ofsmall molecules on gidA1 polypeptide self-association as well as anassociation of gidA1 polypeptide and another polypeptide or smallmolecule. GidA1 polypeptide can be coupled to a sensor chip at low sitedensity such that covalently bound molecules will be monomeric. Solutionprotein can then passed over the gidA1 polypeptide-coated surface andspecific binding can be detected in real-time by monitoring the changein resonance angle caused by a change in local refractive index. Thistechnique can be used to characterize the effect of small molecules onkinetic rates and equilibrium binding constants for gidA1 polypeptideself-association as well as an association of gidA1 polypeptide andanother polypeptide or small molecule.

[0131] A scintillation proximity assay may be used to characterize theinteraction between an association of gidA1 polypeptide with anothergidA1 polypeptide or a different polypeptide. gidA1 polypeptide can becoupled to a scintillation-filled bead. Addition of radio-labeled gidA1polypeptide results in binding where the radioactive source molecule isin close proximity to the scintillation fluid. Thus, signal is emittedupon gidA1 polypeptide binding and compounds that prevent gidA1polypeptide self-association or an association of gidA1 polypeptide andanother polypeptide or small molecule will diminish signal.

[0132] ICS biosensors have been described by AMBRI (Australian MembraneBiotechnology Research Institute). They couple the self-association ofmacromolecules to the closing of gramacidin-facilitated ion channels insuspended membrane bilayers and hence to a measurable change in theadmittance (similar to impedence) of the biosensor. This approach islinear over six decades of admittance change and is ideally suited forlarge scale, high through-put screening of small molecule combinatoriallibraries.

[0133] In other embodiments of the invention there are provided methodsfor identifying compounds which bind to or otherwise interact with andinhibit or activate an activity or expression of a polypeptide and/orpolynucleotide of the invention comprising: contacting a polypeptideand/or polynucleotide of the invention with a compound to be screenedunder conditions to permit binding to or other interaction between thecompound and the polypeptide and/or polynucleotide to assess the bindingto or other interaction with the compound, such binding or interactionpreferably being associated with a second component capable of providinga detectable signal in response to the binding or interaction of thepolypeptide and/or polynucleotide with the compound; and determiningwhether the compound binds to or otherwise interacts with and activatesor inhibits an activity or expression of the polypeptide and/orpolynucleotide by detecting the presence or absence of a signalgenerated from the binding or interaction of the compound with thepolypeptide and/or polynucleotide.

[0134] Another example of an assay for gidA1 agonists is a competitiveassay that combines gidA1 and a potential agonist with gidA1-bindingmolecules, recombinant gidA1 binding molecules, natural substrates orligands, or substrate or ligand mimetics, under appropriate conditionsfor a competitive inhibition assay. GidA1 can be labeled, such as byradioactivity or a calorimetric compound, such that the number of gidA1molecules bound to a binding molecule or converted to product can bedetermined accurately to assess the effectiveness of the potentialantagonist.

[0135] Potential antagonists include, among others, small organicmolecules, peptides, polypeptides and antibodies that bind to apolynucleotide and/or polypeptide of the invention and thereby inhibitor extinguish its activity or expression. Potential antagonists also maybe small organic molecules, a peptide, a polypeptide such as a closelyrelated protein or antibody that binds the same sites on a bindingmolecule, such as a binding molecule, without inducing gidA1-inducedactivities, thereby preventing the action or expression of gidA1polypeptides and/or polynucleotides by excluding gidA1 polypeptidesand/or polynucleotides from binding.

[0136] Potential antagonists include a small molecule that binds to andoccupies the binding site of the polypeptide thereby preventing bindingto cellular binding molecules, such that normal biological activity isprevented. Examples of small molecules include but are not limited tosmall organic molecules, peptides or peptide-like molecules. Otherpotential antagonists include antisense molecules (see Okano, J.Neurochem. 56: 560 (1991); OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORSOF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988), for adescription of these molecules). Preferred potential antagonists includecompounds related to and variants of gidA1. Other examples of potentialpolypeptide antagonists include antibodies or, in some cases,oligonucleotides or proteins which are closely related to the ligands,substrates, receptors, enzymes, etc., as the case may be, of thepolypeptide, e.g., a fragment of the ligands, substrates, receptors,enzymes, etc.; or small molecules which bind to the polypeptide of thepresent invention but do not elicit a response, so that the activity ofthe polypeptide is prevented.

[0137] Certain of the polypeptides of the invention are biomimetics,functional mimetics of the natural gidA1 polypeptide. These functionalmimetics may be used for, among other things, antagonizing the activityof gidA1 polypeptide or as a antigen or immunogen in a manner describedelsewhere herein. Functional mimetics of the polypeptides of theinvention include but are not limited to truncated polypeptides. Forexample, preferred functional mimetics include, a polypeptide comprisingthe polypeptide sequence set forth in SEQ ID NO:2 lacking 20, 30, 40,50, 60, 70 or 80 amino- or carboxy-terminal amino acid residues,including fusion proteins comprising one or more of these truncatedsequences Polynucleotides encoding each of these functional mimetics maybe used as expression cassettes to express each mimetic polypeptide. Itis preferred that these cassettes comprise 5′ and 3′ restriction sitesto allow for a convenient means to ligate the cassettes together whendesired. It is further preferred that these cassettes comprise geneexpression signals known in the art or described elsewhere herein.

[0138] Thus, in another aspect, the present invention relates to ascreening kit for identifying agonists, antagonists, ligands, receptors,substrates, enzymes, etc. for a polypeptide and/or polynucleotide of thepresent invention; or compounds which decrease or enhance the productionof such polypeptides and/or polynucleotides, which comprises:

[0139] (a) a polypeptide and/or a polynucleotide of the presentinvention;

[0140] (b) a recombinant cell expressing a polypeptide and/orpolynucleotide of the present invention;

[0141] (c) a cell membrane expressing a polypeptide and/orpolynucleotide of the present invention; or

[0142] (d) antibody to a polypeptide and/or polynucleotide of thepresent invention; which polypeptide is preferably that of SEQ ID NO:2,and which polynucleotide is preferably that of SEQ ID NO:1.

[0143] It will be appreciated that in any such kit, (a), (b), (c) or (d)may comprise a substantial component.

[0144] It will be readily appreciated by the skilled artisan that apolypeptide and/or polynucleotide of the present invention may also beused in a method for the structure-based design of an agonist,antagonist or inhibitor of the polypeptide and/or polynucleotide, by:

[0145] (a) determining in the first instance the three-dimensionalstructure of the polypeptide and/or polynucleotide, or complexesthereof,

[0146] (b) deducing the three-dimensional structure for the likelyreactive site(s), binding site(s) or motif(s) of an agonist, antagonistor inhibitor;

[0147] (c) synthesizing candidate compounds that are predicted to bindto or react with the deduced binding site(s), reactive site(s), and/ormotif(s); and

[0148] (d) testing whether the candidate compounds are indeed agonists,antagonists or inhibitors. It will be further appreciated that this willnormally be an iterative process, and this iterative process may beperformed using automated and computer-controlled steps.

[0149] In a further aspect, the present invention provides methods oftreating abnormal conditions such as, for instance, a Disease, relatedto either an excess of, an under-expression of, an elevated activity of,or a decreased activity of gidA1 polypeptide and/or polynucleotide.

[0150] If the expression and/or activity of the polypeptide and/orpolynucleotide is in excess, several approaches are available. Oneapproach comprises administering to an individual in need thereof aninhibitor compound (antagonist) as herein described, optionally incombination with a pharmaceutically acceptable carrier, in an amounteffective to inhibit the function and/or expression of the polypeptideand/or polynucleotide, such as, for example, by blocking the binding ofligands, substrates, receptors, enzymes, etc., or by inhibiting a secondsignal, and thereby alleviating the abnormal condition. In anotherapproach, soluble forms of the polypeptides still capable of binding theligand, substrate, enzymes, receptors, etc. in competition withendogenous polypeptide and/or polynucleotide may be administered.Typical examples of such competitors include fragments of the gidA1polypeptide and/or polypeptide.

[0151] In a further aspect, the present invention relates to geneticallyengineered soluble fusion proteins comprising a polypeptide of thepresent invention, or a fragment thereof, and various portions of theconstant regions of heavy or light chains of immunoglobulins of varioussubclasses (IgG, IgM, IgA, IgE). Preferred as an immunoglobulin is theconstant part of the heavy chain of human IgG, particularly IgG1, wherefusion takes place at the hinge region. In a particular embodiment, theFc part can be removed simply by incorporation of a cleavage sequencewhich can be cleaved with blood clotting factor Xa. Furthermore, thisinvention relates to processes for the preparation of these fusionproteins by genetic engineering, and to the use thereof for drugscreening, diagnosis and therapy. A further aspect of the invention alsorelates to polynucleotides encoding such fusion proteins. Examples offusion protein technology can be found in International PatentApplication Nos. WO94/29458 and WO94/22914.

[0152] In still another approach, expression of the gene encodingendogenous gidA1 polypeptide can be inhibited using expression blockingtechniques. This blocking may be targeted against any step in geneexpression, but is preferably targeted against transcription and/ortranslation. An examples of a known technique of this sort involve theuse of antisense sequences, either internally generated or separatelyadministered (see, for example, O' Connor, J Neurochem (1991) 56:560 inOligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRCPress, Boca Raton, Fla. (1988)). Alternatively, oligonucleotides whichform triple helices with the gene can be supplied (see, for example, Leeet al., Nucleic Acids Res (1979) 6:3073; Cooney et al., Science (1988)241:456; Dervan et al., Science (1991) 251:1360). These oligomers can beadministered per se or the relevant oligomers can be expressed in vivo.

[0153] Each of the polynucleotide sequences provided herein may be usedin the discovery and development of antibacterial compounds. The encodedprotein, upon expression, can be used as a target for the screening ofantibacterial drugs. Additionally, the polynucleotide sequences encodingthe amino terminal regions of the encoded protein or Shine-Delgarno orother translation facilitating sequences of the respective mRNA can beused to construct antisense sequences to control the expression of thecoding sequence of interest.

[0154] The invention also provides the use of the polypeptide,polynucleotide, agonist or antagonist of the invention to interfere withthe initial physical interaction between a pathogen or pathogens and aeukaryotic, preferably mammalian, host responsible for sequelae ofinfection. In particular, the molecules of the invention may be used: inthe prevention of adhesion of bacteria, in particular gram positiveand/or gram negative bacteria, to eukaryotic, preferably mammalian,extracellular matrix proteins on in-dwelling devices or to extracellularmatrix proteins in wounds; to block bacterial adhesion betweeneukaryotic, preferably mammalian, extracellular matrix proteins andbacterial gidA1 proteins that mediate tissue damage and/or; to block thenormal progression of pathogenesis in infections initiated other than bythe implantation of in-dwelling devices or by other surgical techniques.

[0155] In accordance with yet another aspect of the invention, there areprovided gidA1 agonists and antagonists, preferably bacteristatic orbactericidal agonists and antagonists.

[0156] The antagonists and agonists of the invention may be employed,for instance, to prevent, inhibit and/or treat diseases.

[0157]Helicobacter pylori (herein “H. pylori”) bacteria infect thestomachs of over one-third of the world's population causing stomachcancer, ulcers, and gastritis (International Agency for Research onCancer (1994) Schistosomes, Liver Flukes and Helicobacter Pylori(International Agency for Research on Cancer, Lyon, France,http://www.uicc.chl/ecp/ecp2904.htm). Moreover, the International Agencyfor Research on Cancer recently recognized a cause-and-effectrelationship between H. pylori and gastric adenocarcinoma, classifyingthe bacterium as a Group I (definite) carcinogen. Preferredantimicrobial compounds of the invention (agonists and antagonists ofgidA1 polypeptides and/or polynucleotides) found using screens providedby the invention, or known in the art, particularly narrow-spectrumantibiotics, should be useful in the treatment of H. pylori infection.Such treatment should decrease the advent of H. pylori-induced cancers,such as gastrointestinal carcinoma. Such treatment should also prevent,inhibit and/or cure gastric ulcers and gastritis.

[0158] Vaccines

[0159] There are provided by the invention, products, compositions andmethods for assessing gidA1 expression, treating disease, assayinggenetic variation, and administering a gidA1 polypeptide and/orpolynucleotide to an organism to raise an immunological response againsta bacteria, especially a Streptococcus pneumoniae bacteria.

[0160] Another aspect of the invention relates to a method for inducingan immunological response in an individual, particularly a mammal whichcomprises inoculating the individual with gidA1 polynucleotide and/orpolypeptide, or a fragment or variant thereof, adequate to produceantibody and/or T cell immune response to protect said individual frominfection, particularly bacterial infection and most particularlyStreptococcus pneumoniae infection. Also provided are methods wherebysuch immunological response slows bacterial replication. Yet anotheraspect of the invention relates to a method of inducing immunologicalresponse in an individual which comprises delivering to such individuala nucleic acid vector, sequence or ribozyme to direct expression ofgidA1 polynucleotide and/or polypeptide, or a fragment or a variantthereof, for expressing gidA1 polynucleotide and/or polypeptide, or afragment or a variant thereof in vivo in order to induce animmunological response, such as, to produce antibody and/or T cellimmune response, including, for example, cytokine-producing T cells orcytotoxic T cells, to protect said individual, preferably a human, fromdisease, whether that disease is already established within theindividual or not. One example of administering the gene is byaccelerating it into the desired cells as a coating on particles orotherwise. Such nucleic acid vector may comprise DNA, RNA, a ribozyme, amodified nucleic acid, a DNA/RNA hybrid, a DNA-protein complex or anRNA-protein complex.

[0161] A further aspect of the invention relates to an immunologicalcomposition that when introduced into an individual, preferably a human,capable of having induced within it an immunological response, inducesan immunological response in such individual to a gidA1 polynucleotideand/or polypeptide encoded therefrom, wherein the composition comprisesa recombinant gidA1 polynucleotide and/or polypeptide encoded therefromand/or comprises DNA and/or RNA which encodes and expresses an antigenof said gidA1 polynucleotide, polypeptide encoded therefrom, or otherpolypeptide of the invention. The immunological response may be usedtherapeutically or prophylactically and may take the form of antibodyimmunity and/or cellular immunity, such as cellular immunity arisingfrom CTL or CD4+ T cells.

[0162] A gidA1 polypeptide or a fragment thereof may be fused withco-protein or chemical moiety which may or may not by itself produceantibodies, but which is capable of stabilizing the first protein andproducing a fused or modified protein which will have antigenic and/orimmunogenic properties, and preferably protective properties. Thus fusedrecombinant protein, preferably further comprises an antigenicco-protein, such as lipoprotein D from Hemophilus influenzae,Glutathione-S-transferase (GST) or beta-galactosidase, or any otherrelatively large co-protein which solubilizes the protein andfacilitates production and purification thereof. Moreover, theco-protein may act as an adjuvant in the sense of providing ageneralized stimulation of the immune system of the organism receivingthe protein. The co-protein may be attached to either the amino- orcarboxy-terminus of the first protein.

[0163] Provided by this invention are compositions, particularly vaccinecompositions, and methods comprising the polypeptides and/orpolynucleotides of the invention and immunostimulatory DNA sequences,such as those described in Sato, Y. et al. Science 273: 352 (1996).

[0164] Also, provided by this invention are methods using the describedpolynucleotide or particular fragments thereof, which have been shown toencode non-variable regions of bacterial cell surface proteins, inpolynucleotide constructs used in such genetic inmunization experimentsin animal models of infection with Streptococcus pneumoniae. Suchexperiments will be particularly useful for identifying protein epitopesable to provoke a prophylactic or therapeutic immune response. It isbelieved that this approach will allow for the subsequent preparation ofmonoclonal antibodies of particular value, derived from the requisiteorgan of the animal successfully resisting or clearing infection, forthe development of prophylactic agents or therapeutic treatments ofbacterial infection, particularly Streptococcus pneumoniae infection, inmammals, particularly humans.

[0165] A polypeptide of the invention may be used as an antigen forvaccination of a host to produce specific antibodies which protectagainst invasion of bacteria, for example by blocking adherence ofbacteria to damaged tissue. Examples of tissue damage include wounds inskin or connective tissue caused, for example, by mechanical, chemical,thermal or radiation damage or by implantation of indwelling devices, orwounds in the mucous membranes, such as the mouth, throat, mammaryglands, urethra or vagina.

[0166] The invention also includes a vaccine formulation which comprisesan immunogenic recombinant polypeptide and/or polynucleotide of theinvention together with a suitable carrier, such as a pharmaceuticallyacceptable carrier. Since the polypeptides and polynucleotides may bebroken down in the stomach, each is preferably administeredparenterally, including, for example, administration that issubcutaneous, intramuscular, intravenous, or intradermal. Formulationssuitable for parenteral administration include aqueous and non-aqueoussterile injection solutions which may contain anti-oxidants, buffers,bacteristatic compounds and solutes which render the formulationisotonic with the bodily fluid, preferably the blood, of the individual;and aqueous and non-aqueous sterile suspensions which may includesuspending agents or thickening agents. The formulations may bepresented in unit-dose or multi-dose containers, for example, sealedampoules and vials and may be stored in a freeze-dried conditionrequiring only the addition of the sterile liquid carrier immediatelyprior to use. The vaccine formulation may also include adjuvant systemsfor enhancing the immunogenicity of the formulation, such as oil-inwater systems and other systems known in the art. The dosage will dependon the specific activity of the vaccine and can be readily determined byroutine experimentation.

[0167] While the invention has been described with reference to certaingidA1 polypeptides and polynucleotides, it is to be understood that thiscovers fragments of the naturally occurring polypeptides andpolynucleotides, and similar polypeptides and polynucleotides withadditions, deletions or substitutions which do not substantially affectthe immunogenic properties of the recombinant polypeptides orpolynucleotides.

[0168] Compositions, Kits and Administration

[0169] In a further aspect of the invention there are providedcompositions comprising a gidA1 polynucleotide and/or a gidA1polypeptide for administration to a cell or to a multicellular organism.

[0170] The invention also relates to compositions comprising apolynucleotide and/or a polypeptides discussed herein or their agonistsor antagonists. The polypeptides and polynucleotides of the inventionmay be employed in combination with a non-sterile or sterile carrier orcarriers for use with cells, tissues or organisms, such as apharmaceutical carrier suitable for administration to an individual.Such compositions comprise, for instance, a media additive or atherapeutically effective amount of a polypeptide and/or polynucleotideof the invention and a pharmaceutically acceptable carrier or excipient.Such carriers may include, but are not limited to, saline, bufferedsaline, dextrose, water, glycerol, ethanol and combinations thereof. Theformulation should suit the mode of administration. The inventionfurther relates to diagnostic and pharmaceutical packs and kitscomprising one or more containers filled with one or more of theingredients of the aforementioned compositions of the invention.

[0171] Polypeptides, polynucleotides and other compounds of theinvention may be employed alone or in conjunction with other compounds,such as therapeutic compounds.

[0172] The pharmaceutical compositions may be administered in anyeffective, convenient manner including, for instance, administration bytopical, oral, anal, vaginal, intravenous, intraperitoneal,intramuscular, subcutaneous, intranasal or intradermal routes amongothers.

[0173] In therapy or as a prophylactic, the active agent may beadministered to an individual as an injectable composition, for exampleas a sterile aqueous dispersion, preferably isotonic.

[0174] Alternatively the composition may be formulated for topicalapplication for example in the form of ointments, creams, lotions, eyeointments, eye drops, ear drops, mouthwash, impregnated dressings andsutures and aerosols, and may contain appropriate conventionaladditives, including, for example, preservatives, solvents to assistdrug penetration, and emollients in ointments and creams. Such topicalformulations may also contain compatible conventional carriers, forexample cream or ointment bases, and ethanol or oleyl alcohol forlotions. Such carriers may constitute from about 1% to about 98% byweight of the formulation; more usually they will constitute up to about80% by weight of the formulation.

[0175] In a further aspect, the present invention provides forpharmaceutical compositions comprising a therapeutically effectiveamount of a polypeptide and/or polynucleotide, such as the soluble formof a polypeptide and/or polynucleotide of the present invention, agonistor antagonist peptide or small molecule compound, in combination with apharmaceutically acceptable carrier or excipient. Such carriers include,but are not limited to, saline, buffered saline, dextrose, water,glycerol, ethanol, and combinations thereof The invention furtherrelates to pharmaceutical packs and kits comprising one or morecontainers filled with one or more of the ingredients of theaforementioned compositions of the invention. Polypeptides,polynucleotides and other compounds of the present invention may beemployed alone or in conjunction with other compounds, such astherapeutic compounds.

[0176] The composition will be adapted to the route of administration,for instance by a systemic or an oral route Preferred forms of systemicadministration include injection, typically by intravenous injection.Other injection routes, such as subcutaneous, intramuscular, orintraperitoneal, can be used. Alternative means for systemicadministration include transmucosal and transdermal administration usingpenetrants such as bile salts or fusidic acids or other detergents. Inaddition, if a polypeptide or other compounds of the present inventioncan be formulated in an enteric or an encapsulated formulation, oraladministration may also be possible. Administration of these compoundsmay also be topical and/or localized, in the form of salves, pastes,gels, and the like.

[0177] For administration to mammals, and particularly humans, it isexpected that the daily dosage level of the active agent will be from0.01 mg/kg to 10 mg/kg, typically around 1 mg/kg. The physician in anyevent will determine the actual dosage which will be most suitable foran individual and will vary with the age, weight and response of theparticular individual. The above dosages are exemplary of the averagecase. There can, of course, be individual instances where higher orlower dosage ranges are merited, and such are within the scope of thisinvention.

[0178] In-dwelling devices include surgical implants, prosthetic devicesand catheters, i.e., devices that are introduced to the body of anindividual and remain in position for an extended time. Such devicesinclude, for example, artificial joints, heart valves, pacemakers,vascular grafts, vascular catheters, cerebrospinal fluid shunts, urinarycatheters, continuous ambulatory peritoneal dialysis (CAPD) catheters.

[0179] The composition of the invention may be administered by injectionto achieve a systemic effect against relevant bacteria shortly beforeinsertion of an in-dwelling device. Treatment may be continued aftersurgery during the in-body time of the device. In addition, thecomposition could also be used to broaden perioperative cover for anysurgical technique to prevent bacterial wound infections, especiallyStreptococcus pneumoniae wound infections.

[0180] Many orthopedic surgeons consider that humans with prostheticjoints should be considered for antibiotic prophylaxis before dentaltreatment that could produce a bacteremia. Late deep infection is aserious complication sometimes leading to loss of the prosthetic jointand is accompanied by significant morbidity and mortality. It maytherefore be possible to extend the use of the active agent as areplacement for prophylactic antibiotics in this situation.

[0181] In addition to the therapy described above, the compositions ofthis invention may be used generally as a wound treatment agent toprevent adhesion of bacteria to matrix proteins exposed in wound tissueand for prophylactic use in dental treatment as an alternative to, or inconjunction with antibiotic prophylaxis.

[0182] Alternatively, the composition of the invention may be used tobathe an indwelling device immediately before insertion. The activeagent will preferably be present at a concentration of 1 μg/ml to 10mg/ml for bathing of wounds or indwelling devices.

[0183] A vaccine composition is conveniently in injectable form.Conventional adjuvants may be employed to enhance the immune response. Asuitable unit dose for vaccination is 0.5-5 microgram/kg of antigen, andsuch dose is preferably administered 1-3 times and with an interval of1-3 weeks. With the indicated dose range, no adverse toxicologicaleffects will be observed with the compounds of the invention which wouldpreclude their administration to suitable individuals.

[0184] Sequence Databases, Sequences in a Tangible Medium, andAlgorithms

[0185] Polynucleotide and polypeptide sequences form a valuableinformation resource with which to determine their 2- and 3-dimensionalstructures as well as to identify further sequences of similar homology.These approaches are most easily facilitated by storing the sequence ina computer readable medium and then using the stored data in a knownmacromolecular structure program or to search a sequence database usingwell known searching tools, such as GCC.

[0186] The polynucleotide and polypeptide sequences of the invention areparticularly useful as components in databases useful for searchanalyses as well as in sequence analysis algorithms. As used in thissection entitled “Sequence Databases, Sequences in a Tangible Medium,and Algorithms,” and in claims related to this section, the terms“polynucleotide of the invention” and “polynucleotide sequence of theinvention” mean any detectable chemical or physical characteristic of apolynucleotide of the invention that is or may be reduced to or storedin a tangible medium, preferably a computer readable form. For example,chromatographic scan data or peak data, photographic data or scan datatherefrom, called bases, and mass spectrographic data. As used in thissection entitled Databases and Algorithms and in claims related thereto,the terms “polypeptide of the invention” and “polypeptide sequence ofthe invention” mean any detectable chemical or physical characteristicof a polypeptide of the invention that is or may be reduced to or storedin a tangible medium, preferably a computer readable form. For example,chromatographic scan data or peak data, photographic data or scan datatherefrom, and mass spectrographic data.

[0187] The invention provides a computer readable medium having storedthereon polypeptide sequences of the invention and/or polynucleotidesequences of the invention. For example, a computer readable medium isprovided comprising and having stored thereon a member selected from thegroup consisting of: a polynucleotide comprising the sequence of apolynucleotide of the invention; a polypeptide comprising the sequenceof a polypeptide sequence of the invention; a set of polynucleotidesequences wherein at least one of the sequences comprises the sequenceof a polynucleotide sequence of the invention; a set of polypeptidesequences wherein at least one of the sequences comprises the sequenceof a polypeptide sequence of the invention; a data set representing apolynucleotide sequence comprising the sequence of polynucleotidesequence of the invention; a data set representing a polynucleotidesequence encoding a polypeptide sequence comprising the sequence of apolypeptide sequence of the invention; a polynucleotide comprising thesequence of a polynucleotide sequence of the invention; a polypeptidecomprising the sequence of a polypeptide sequence of the invention; aset of polynucleotide sequences wherein at least one of the sequencescomprises the sequence of a polynucleotide sequence of the invention, aset of polypeptide sequences wherein at least one of said sequencescomprises the sequence of a polypeptide sequence of the invention; adata set representing a polynucleotide sequence comprising the sequenceof a polynucleotide sequence of the invention; a data set representing apolynucleotide sequence encoding a polypeptide sequence comprising thesequence of a polypeptide sequence of the invention. The computerreadable medium can be any composition of matter used to storeinformation or data, including, for example, commercially availablefloppy disks, tapes, chips, hard drives, compact disks, and video disks.

[0188] Also provided by the invention are methods for the analysis ofcharacter sequences or strings, particularly genetic sequences orencoded genetic sequences. Preferred methods of sequence analysisinclude, for example, methods of sequence homology analysis, such asidentity and similarity analysis, RNA structure analysis, sequenceassembly, cladistic analysis, sequence motif analysis, open readingframe determination, nucleic acid base calling, nucleic acid basetrimming, and sequencing chromatogram peak analysis.

[0189] A computer based method is provided for performing homologyidentification. This method comprises the steps of providing a firstpolynucleotide sequence comprising the sequence a polynucleotide of theinvention in a computer readable medium; and comparing said firstpolynucleotide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

[0190] A computer based method is also provided for performing homologyidentification, said method comprising the steps of: providing a firstpolypeptide sequence comprising the sequence of a polypeptide of theinvention in a computer readable medium; and comparing said firstpolypeptide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

[0191] A computer based method is still further provided forpolynucleotide assembly, said method comprising the steps of: providinga first polynucleotide sequence comprising the sequence of apolynucleotide of the invention in a computer readable medium; andscreening for at least one overlapping region between said firstpolynucleotide sequence and at least one second polynucleotide orpolypeptide sequence.

[0192] A computer based method is still further provided forpolynucleotide assembly, said method comprising the steps of: providinga first polypeptide sequence comprising a polypeptide of the inventionin a computer readable medium; and screening for at least oneoverlapping region between said first polypeptide sequence and at leastone second polynucleotide or polypeptide sequence.

[0193] In another preferred embodiment of the invention there isprovided a computer readable medium having stored thereon a memberselected from the group consisting of: a polynucleotide comprising thesequence of SEQ ID NO. 1 or 3; a polypeptide comprising the sequence ofSEQ ID NO. 2 or 4; a set of polynucleotide sequences wherein at leastone of said sequences comprises the sequence of SEQ ID NO. 1 or 3; a setof polypeptide sequences wherein at least one of said sequencescomprises the sequence of SEQ ID NO. 2 or 4; a data set representing apolynucleotide sequence comprising the sequence of SEQ ID NO. 1 or 3; adata set representing a polynucleotide sequence encoding a polypeptidesequence comprising the sequence of SEQ ID NO. 2 or 4; a polynucleotidecomprising the sequence of SEQ ID NO. 1 or 3; a polypeptide comprisingthe sequence of SEQ ID NO. 2 or 4; a set of polynucleotide sequenceswherein at least one of said sequences comprises the sequence of SEQ IDNO. 1 or 3; a set of polypeptide sequences wherein at least one of saidsequences comprises the sequence of SEQ ID NO. 2 or 4; a data setrepresenting a polynucleotide sequence comprising the sequence of SEQ IDNO. 1 or 3; a data set representing a polynucleotide sequence encoding apolypeptide sequence comprising the sequence of SEQ ID NO. 2 or 4. Afurther preferred embodiment of the invention provides a computer basedmethod for performing homology identification, said method comprisingthe steps of providing a polynucleotide sequence comprising the sequenceof SEQ ID NO. 1 or 3 in a computer readable medium; and comparing saidpolynucleotide sequence to at least one polynucleotide or polypeptidesequence to identify homology.

[0194] A still further preferred embodiment of the invention provides acomputer based method for performing homology identification, saidmethod comprising the steps of: providing a polypeptide sequencecomprising the sequence of SEQ ID NO. 2 or 4 in a computer readablemedium; and comparing said polypeptide sequence to at least onepolynucleotide or polypeptide sequence to identify homology.

[0195] A further embodiment of the invention provides a computer basedmethod for polynucleotide assembly, said method comprising the steps of:providing a first polynucleotide sequence comprising the sequence of SEQID NO. 1 or 3 in a computer readable medium; and screening for at leastone overlapping region between said first polynucleotide sequence and asecond polynucleotide sequence.

[0196] A further embodiment of the invention provides a computer basedmethod for performing homology identification, said method comprisingthe steps of: providing a polynucleotide sequence comprising thesequence of SEQ ID NO. 1 or 3 in a computer readable medium; andcomparing said polynucleotide sequence to at least one polynucleotide orpolypeptide sequence to identify homology.

[0197] All publications and references, including but not limited topatents and patent applications, cited in this specification are hereinincorporated by reference in their entirety as if each individualpublication or reference were specifically and individually indicated tobe incorporated by reference herein as being fully set forth. Any patentapplication to which this application claims priority is alsoincorporated by reference herein in its entirety in the manner describedabove for publications and references.

[0198] Glossary

[0199] The following definitions are provided to facilitateunderstanding of certain terms used frequently herein.

[0200] “Antibody(ies)” as used herein includes polyclonal and monoclonalantibodies, chimeric, single chain, and humanized antibodies, as well asFab fragments, including the products of an Fab or other immunoglobulinexpression library.

[0201] “Antigenically equivalent derivative(s)” as used hereinencompasses a polypeptide, polynucleotide, or the equivalent of eitherwhich will be specifically recognized by certain antibodies which, whenraised to the protein, polypeptide or polynucleotide according to theinvention, interferes with the immediate physical interaction betweenpathogen and mammalian host.

[0202] “Bispecific antibody(ies)” means an antibody comprising at leasttwo antigen binding domains, each domain directed against a differentepitope.

[0203] “Bodily material(s) means any material derived from an individualor from an organism infecting, infesting or inhabiting an individual,including but not limited to, cells, tissues and waste, such as, bone,blood, serum, cerebrospinal fluid, semen, saliva, muscle, cartilage,organ tissue, skin, urine, stool or autopsy materials.

[0204] “Disease(s)” means any disease caused by or related to infectionby a bacteria, including, for example, otitis media, conjunctivitis,pneumonia, bacteremia, meningitis, sinusitis, pleural empyema andendocarditis, and most particularly meningitis, such as for exampleinfection of cerebrospinal fluid.

[0205] “Fusion protein(s)” refers to a protein encoded by two, oftenunrelated, fused genes or fragments thereof. In one example, EP-A-0464discloses fusion proteins comprising various portions of constant regionof immunoglobulin molecules together with another human protein or partthereof. In many cases, employing an immunoglobulin Fc region as a partof a fusion protein is advantageous for use in therapy and diagnosisresulting in, for example, improved pharmacokinetic properties [see,e.g., EP-A 0232262]. On the other hand, for some uses it would bedesirable to be able to delete the Fe part after the fusion protein hasbeen expressed, detected and purified.

[0206] “Host cell(s)” is a cell which has been transformed ortransfected, or is capable of transformation or transfection by anexogenous polynucleotide sequence.

[0207] “Identity,” as known in the art, is a relationship between two ormore polypeptide sequences or two or more polynucleotide sequences, asthe case may be, as determined by comparing the sequences. In the art,“identity” also means the degree of sequence relatedness betweenpolypeptide or polynucleotide sequences, as the case may be, asdetermined by the match between strings of such sequences “Identity” canbe readily calculated by known methods, including but not limited tothose described in (Computational Molecular Biology, Lesk, A. M., ed.,Oxford University Press, New York, 1988; Biocomputing: Informatics andGenome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin,H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis inMolecular Biology, von Heinje, G., Academic Press, 1987; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991; and Carillo, H., and Lipman, D., SIAM J Applied Math.,48: 1073 (1988). Methods to determine identity are designed to give thelargest match between the sequences tested. Moreover, methods todetermine identity are codified in publicly available computer programs.Computer program methods to determine identity between two sequencesinclude, but are not limited to, the GCG program package (Devereux, J.,et al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP. BLASTN, andFASTA (Altschul, S. F. et al., J. Molec. Biol. 215: 403-410 (1990). TheBLAST X program is publicly available from NCBI and other sources(BLASTManual, Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894;Altschul, S , et al., J. Mol. Biol. 215: 403-410 (1990). The well knownSmith Waterman algorithm may also be used to determine identity.

[0208] Parameters for polypeptide sequence comparison include thefollowing:

[0209] 1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453(1970)

[0210] Comparison matrix: BLOSSUM62 from Hentikoff and Hentikoff, Proc.Natl. Acad. Sci. USA. 89:10915-10919 (1992)

[0211] Gap Penalty: 12

[0212] Gap Length Penalty: 4

[0213] A program useful with these parameters is publicly available asthe “gap” program from Genetics Computer Group, Madison Wis. Theaforementioned parameters are the default parameters for peptidecomparisons (along with no penalty for end gaps).

[0214] Parameters for polynucleotide comparison include the following:

[0215] 1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453(1970)

[0216] Comparison matrix: matches=+10, mismatch=0

[0217] Gap Penalty: 50

[0218] Gap Length Penalty: 3

[0219] Available as: The “gap” program from Genetics Computer Group,Madison Wis. These are the default parameters for nucleic acidcomparisons.

[0220] A preferred meaning for “identity” for polynucleotides andpolypeptides, as the case may be, are provided in (1) and (2) below.

[0221] (1) Polynucleotide embodiments further include an isolatedpolynucleotide comprising a polynucleotide sequence having at least a50, 60, 70, 80, 85, 90, 95, 97 or 100% identity to the referencesequence of SEQ ID NO: 1, wherein said polynucleotide sequence may beidentical to the reference sequence of SEQ ID NO: 1 or may include up toa certain integer number of nucleotide alterations as compared to thereference sequence, wherein said alterations are selected from the groupconsisting of at least one nucleotide deletion, substitution, includingtransition and transversion, or insertion, and wherein said alterationsmay occur at the 5′ or 3′ terminal positions of the reference nucleotidesequence or anywhere between those terminal positions, interspersedeither individually among the nucleotides in the reference sequence orin one or more contiguous groups within the reference sequence, andwherein said number of nucleotide alterations is determined bymultiplying the total number of nucleotides in SEQ ID NO: 1 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of nucleotides in SEQ IDNO: 1, or:

n _(n) ≦x _(n)−(x _(n) ·y),

[0222] wherein n_(n) is the number of nucleotide alterations, x_(n) isthe total number of nucleotides in SEQ ID NO:1, y is 0.50 for 50%, 0.60for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95for 95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n). Alterations of a polynucleotide sequence encoding thepolypeptide of SEQ ID NO:2 may create nonsense, missense or frameshiftmutations in this coding sequence and thereby alter the polypeptideencoded by the polynucleotide following such alterations.

[0223] By way of example, a polynucleotide sequence of the presentinvention may be identical to the reference sequence of SEQ ID NO:1,that is it may be 100% identical, or it may include up to a certaininteger number of nucleic acid alterations as compared to the referencesequence such that the percent identity is less than 100% identity. Suchalterations are selected from the group consisting of at least onenucleic acid deletion, substitution, including transition andtransversion, or insertion, and wherein said alterations may occur atthe 5′ or 3′ terminal positions of the reference polynucleotide sequenceor anywhere between those terminal positions, interspersed eitherindividually among the nucleic acids in the reference sequence or in oneor more contiguous groups within the reference sequence. The number ofnucleic acid alterations for a given percent identity is determined bymultiplying the total number of nucleic acids in SEQ ID NO:1 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of nucleic acids in SEQID NO:1, or.

n _(n) ≦x _(n)−(x _(n) ·y),

[0224] wherein n_(n) is the number of nucleic acid alterations, x_(n) isthe total number of nucleic acids in SEQ ID NO:1, y is, for instance0.70 for 70%, 0.80 for 80%, 0.85 for 85% etc., · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n).

[0225] (2) Polypeptide embodiments further include an isolatedpolypeptide comprising a polypeptide having at least a 50,60, 70, 80,85, 90, 95, 97 or 100% identity to a polypeptide reference sequence ofSEQ ID NO:2, wherein said polypeptide sequence may be identical to thereference sequence of SEQ ID NO: 2 or may include up to a certaininteger number of amino acid alterations as compared to the referencesequence, wherein said alterations are selected from the groupconsisting of at least one amino acid deletion, substitution, includingconservative and non-conservative substitution, or insertion, andwherein said alterations may occur at the amino- or carboxy-terminalpositions of the reference polypeptide sequence or anywhere betweenthose terminal positions, interspersed either individually among theamino acids in the reference sequence or in one or more contiguousgroups within the reference sequence, and wherein said number of aminoacid alterations is determined by multiplying the total number of aminoacids in SEQ ID NO:2 by the integer defining the percent identitydivided by 100 and then subtracting that product from said total numberof amino acids in SEQ ID NO:2, or:

n _(a) ≦x _(a)−(x _(a) ·y)

[0226] wherein n_(a) is the number of amino acid alterations, x_(a) isthe total number of amino acids in SEQ ID NO:2, y is 0.50 for 50%, 0.60for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95for 95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

[0227] By way of example, a polypeptide sequence of the presentinvention may be identical to the reference sequence of SEQ ID NO:2,that is it may be 100% identical, or it may include up to a certaininteger number of amino acid alterations as compared to the referencesequence such that the percent identity is less than 100% identity. Suchalterations are selected from the group consisting of at least one aminoacid deletion, substitution, including conservative and non-conservativesubstitution, or insertion, and wherein said alterations may occur atthe amino- or carboxy-terminal positions of the reference polypeptidesequence or anywhere between those terminal positions, interspersedeither individually among the amino acids in the reference sequence orin one or more contiguous groups within the reference sequence. Thenumber of amino acid alterations for a given % identity is determined bymultiplying the total number of amino acids in SEQ ID NO:2 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of amino acids in SEQ IDNO:2, or:

n _(a) ≦x _(a)−(x _(a) ·y),

[0228] wherein n_(a) is the number of amino acid alterations, x_(a) isthe total number of amino acids in SEQ ID NO.2. y is, for instance 0.70for 70%, 0.80 for 80%, 0.85 for 85% etc., and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

[0229] “Immunologically equivalent derivative(s)” as used hereinencompasses a polypeptide, polynucleotide, or the equivalent of eitherwhich when used in a suitable formulation to raise antibodies in avertebrate, the antibodies act to interfere with the immediate physicalinteraction between pathogen and mammalian host.

[0230] “Immunospecific” means that characteristic of an antibody wherebyit possesses substantially greater affinity, for the polypeptides of theinvention or the polynucleotides of the invention than its affinity forother related polypeptides or polynucleotides respectively, particularlythose polypeptides and polynucleotides in the prior art.

[0231] “Individual(s)” means a multicellular eukaryote, including, butnot limited to a metazoan, a mammal, an ovid, a bovid, a simian, aprimate, and a human.

[0232] “Isolated” means altered “by the hand of man” from its naturalstate, i.e., if it occurs in nature, it has been changed or removed fromits original environment, or both. For example, a polynucleotide or apolypeptide naturally present in a living organism is not “isolated,”but the same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated”, as the term is employedherein. Moreover, a polynucleotide or polypeptide that is introducedinto an organism by transformation, genetic manipulation or by any otherrecombinant method is “isolated” even if it is still present in saidorganism, which organism may be living or non-living.

[0233] “Organism(s)” means a (i) prokaryote, including but not limitedto, a member of the genus Streptococcus, Staphylococcus, Bordetella,Corynebacterium, Mycobacterium, Neisseria, Haemophlus, Actinomycetes,Streptomycetes, Nocardia, Enterobacter, Yersinia, Fancisella,Pasturella, Moraxella, Acinetobacter, Erysipelothrix, Branhamella,Actinobacillus, Streptobacillus, Listeria, Calymmatobacterium, Brucella,Bacillus, Clostridium, Treponema, Escherichia, Salmonella, Kleibsiella,Vibrio, Proteus, Erwinia, Borrelia, Leptospira, Spirillum,Campylobacter, Shigella, Legionella, Pseudomonas, Aeromonas, Rickettsia,Chlamydia, Borrelia and Mycoplasma, and further including, but notlimited to, a member of the species or group, Group A Streptococcus,Group B Streptococcus, Group C Streptococcus, Group D Streptococcus,Group G Streptococcus, Streptococcus pneumoniae, Streptococcus pyogenes,Streptococcus agalactiae, Streptococcus faecalis, Streptococcus faecium,Streptococcus durans, Neisseria gonorrheae, Neisseria meningitidis,Staphylococcus aureus, Staphylococcus epidermidis, Corynebacteriumdiptheriae, Gardnerella vaginalis, Mycobacterium tuberculosis,Mycobacterium bovis, Mycobacterium ulcerans, Mycobacterium leprae,Actinomyctes israelii, Listeria monocytogenes, Bordetella pertusis,Bordatella parapertusis, Bordetella bronchiseptica, Escherichia coli,Shigella dysenteriae, Haemophilus influenzae, Haemophilus aegyptius,Haemophilus parainfluenzae, Haemophilus ducreyi, Bordetella, Salmonellatyphi, Citrobacter freundii, Proteus mirabilis, Proteus vulgaris,Yersinia pestis, Kleibsiella pneumoniae, Serratia marcessens, Serratialiquefaciens, Vibrio cholera, Shigella dysenterii, Shigella flexneri,Pseudomonas aeruginosa, Franscisella tularensis, Brucella abortis,Bacillus anthracis, Bacillus cereus, Clostridium perfringens,Clostridium tetani, Clostridium botulinum, Treponema pallidum,Rickettsia rickettsii and Chiamydia trachomitis, (ii) an archaeon,including but not limited to Archaebacter, and (iii) a unicellular orfilamentous eukaryote, including but not limited to, a protozoan, afungus, a member of the genus Saccharomyces, Kluveromyces, or Candida,and a member of the species Saccharomyces ceriviseae, Kluveromyceslactis, or Candida albicans.

[0234] “Polynucleotide(s)” generally refers to any polyribonucleotide orpolydeoxyribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA. “Polynucleotide(s)” include, without limitation, single- anddouble-stranded DNA, DNA that is a mixture of single- anddouble-stranded regions or single-, double- and triple-stranded regions,single- and double-stranded RNA, and RNA that is mixture of single- anddouble-stranded regions, hybrid molecules comprising DNA and RNA thatmay be single-stranded or, more typically, double-stranded, ortriple-stranded regions, or a mixture of single- and double-strandedregions. In addition, “polynucleotide” as used herein refers totriple-stranded regions comprising RNA or DNA or both RNA and DNA. Thestrands in such regions may be from the same molecule or from differentmolecules. The regions may include all of one or more of the molecules,but more typically involve only a region of some of the molecules. Oneof the molecules of a triple-helical region often is an oligonucleotide.As used herein, the term “polynucleotide(s)” also includes DNAs or RNAsas described above that contain one or more modified bases. Thus, DNAsor RNAs with backbones modified for stability or for other reasons are“polynucleotide(s)” as that term is intended herein. Moreover, DNAs orRNAs comprising unusual bases, such as inosine, or modified bases, suchas tritylated bases, to name just two examples, are polynucleotides asthe term is used herein. It will be appreciated that a great variety ofmodifications have been made to DNA and RNA that serve many usefulpurposes known to those of skill in the art. The term“polynucleotide(s)” as it is employed herein embraces such chemically,enzymatically or metabolically modified forms of polynucleotides, aswell as the chemical forms of DNA and RNA characteristic of viruses andcells, including, for example, simple and complex cells.“Polynucleotide(s)” also embraces short polynucleotides often referredto as oligonucleotide(s).

[0235] “Polypeptide(s)” refers to any peptide or protein comprising twoor more amino acids joined to each other by peptide bonds or modifiedpeptide bonds. “Polypeptide(s)” refers to both short chains, commonlyreferred to as peptides, oligopeptides and oligomers and to longerchains generally referred to as proteins. Polypeptides may contain aminoacids other than the 20 gene encoded amino acids. “Polypeptide(s)”include those modified either by natural processes, such as processingand other post-translational modifications, but also by chemicalmodification techniques. Such modifications are well described in basictexts and in more detailed monographs, as well as in a voluminousresearch literature, and they are well known to those of skill in theart. It will be appreciated that the same type of modification may bepresent in the same or varying degree at several sites in a givenpolypeptide. Also, a given polypeptide may contain many types ofmodifications. Modifications can occur anywhere in a polypeptide,including the peptide backbone. the amino acid side-chains, and theamino or carboxyl termini Modifications include., for example,acetylation, acylation, ADP-ribosylation, amidation, covalent attachmentof flavin, covalent attachment of a heme moiety, covalent attachment ofa nucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, demethylation,formation of covalent cross-links, formation of cysteine, formation ofpyroglutamate, formylation, gamma-carboxylation, GPI anchor formation,hydroxylation, iodination, methylation, myristoylation, oxidation,proteolytic processing, phosphorylation, prenylation, racemization,glycosylation, lipid attachment, sulfation, gamma-carboxylation ofglutamic acid residues, hydroxylation and ADP-ribosylation,selenoylation, sulfation, transfer-RNA mediated addition of amino acidsto proteins, such as arginylation, and ubiquitination. See, forinstance, PROTEINS—STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E.Creighton, W. H. Freeman and Company, New York (1993) and Wold, F.,Posttranslational Protein Modifications: Perspectives and Prospects,pgs. 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C.Johnson, Ed., Academic Press, New York (1983); Seifter et al., Meth.Enzymol. 182:626-646 (1990) and Rattan et al., Protein Synthesis:Posttranslational Modifications and Aging, Ann. N.Y. Acad. Sci. 663:48-62 (1992). Polypeptides may be branched or cyclic, with or withoutbranching. Cyclic, branched and branched circular polypeptides mayresult from post-translational natural processes and may be made byentirely synthetic methods, as well.

[0236] “Recombinant expression system(s)” refers to expression systemsor portions thereof or polynucleotides of the invention introduced ortransformed into a host cell or host cell lysate for the production ofthe polynucleotides and polypeptides of the invention.

[0237] “Subtraction set” is one or more, but preferably less than 100,polynucleotides comprising at least one polynucleotide of the invention

[0238] “Variant(s)” as the term is used herein, is a polynucleotide orpolypeptide that differs from a reference polynucleotide or polypeptiderespectively, but retains essential properties. A typical variant of apolynucleotide differs in nucleotide sequence from another, referencepolynucleotide. Changes in the nucleotide sequence of the variant may ormay not alter the amino acid sequence of a polypeptide encoded by thereference polynucleotide. Nucleotide changes may result in amino acidsubstitutions, additions, deletions, fusion proteins and truncations inthe polypeptide encoded by the reference sequence, as discussed below. Atypical variant of a polypeptide differs in amino acid sequence fromanother, reference polypeptide. Generally, differences are limited sothat the sequences of the reference polypeptide and the variant areclosely similar overall and, in many regions, identical. A variant andreference polypeptide may differ in amino acid sequence by one or moresubstitutions, additions, deletions in any combination. A substituted orinserted amino acid residue may or may not be one encoded by the geneticcode. The present invention also includes include variants of each ofthe polypeptides of the invention, that is polypeptides that vary fromthe referents by conservative amino acid substitutions, whereby aresidue is substituted by another with like characteristics. Typicalsuch substitutions are among Ala, Val, Leu and Ile; among Ser and Thr;among the acidic residues Asp and Glu; among Asn and Gln; and among thebasic residues Lys and Arg; or aromatic residues Phe and Tyr.Particularly preferred are variants in which several, 5-10, 1-5, 1-3,1-2 or 1 amino acids are substituted, deleted, or added in anycombination. A variant of a polynucleotide or polypeptide may be anaturally occurring such as an allelic variant, or it may be a variantthat is not known to occur naturally. Non-naturally occurring variantsof polynucleotides and polypeptides may be made by mutagenesistechniques, by direct synthesis, and by other recombinant methods knownto skilled artisans.

EXAMPLES

[0239] The examples below are carried out using standard techniques,which are well known and routine to those of skill in the art, exceptwhere otherwise described in detail. The examples are illustrative, butdo not limit the invention.

Example 1 Strain Selection, Library Production and Sequencing

[0240] The polynucleotide having a DNA sequence given in Table 1 [SEQ IDNO:1 or 3] was obtained from a library of clones of chromosomal DNA ofStreptococcus pneumoniae in E. coli. The sequencing data from two ormore clones containing overlapping Streptococcus pneumoniae DNAs wasused to construct the contiguous DNA sequence in SEQ ID NO:1. Librariesmay be prepared by routine methods, for example:

[0241] Methods 1 and 2 below.

[0242] Total cellular DNA is isolated from Streptococcus pneumoniae0100993 according to standard procedures and size-fractionated by eitherof two methods.

[0243] Method 1

[0244] Total cellular DNA is mechanically sheared by passage through aneedle in order to size-fractionate according to standard procedures.DNA fragments of up to 11 kbp in size are rendered blunt by treatmentwith exonuclease and DNA polymerase, and EcoRI linkers added. Fragmentsare ligated into the vector Lambda ZapII that has been cut with EcoRI,the library packaged by standard procedures and E. coli infected withthe packaged library. The library is amplified by standard procedures.

[0245] Method 2

[0246] Total cellular DNA is partially hydrolyzed with a one or acombination of restriction enzymes appropriate to generate a series offragments for cloning into library vectors (e.g., RsaI, PalI. AluI,Bshl235I), and such fragments are size-fractionated according tostandard procedures. EcoRI linkers are ligated to the DNA and thefragments then ligated into the vector Lambda ZapII that have been cutwith EcoRI, the library packaged by standard procedures, and E. coliinfected with the packaged library. The library is amplified by standardprocedures.

Example 2 GidA1 Characterization

[0247] The Determination of Expression During Infection of a Gene fromStreptococcus pneumoniae

[0248] Recently several novel approaches have been described whichpurport to follow global gene expression during infection (Chuang, S. etal., (1993); Mahan, M. J. et al., Science 259:686-688 (1993); Hensel, M.et al., Science 269:400-403 (1995). These new techniques have so farbeen demonstrated with gram negative pathogen infections but not withinfections with gram positives presumably because the much slowerdevelopment of global transposon mutagenesis and suitable vectors neededfor these strategies in these organisms, and in the case of that processdescribed by Chuang, S. et al., J. Bacteriol. 175:2026-2036 (1993) thedifficulty of isolating suitable quantities of bacterial RNA free ofmammalian RNA derived from the infected tissue to furnish bacterial RNAlabelled to sufficiently high specific activity.

[0249] The present invention employs a novel technology to determinegene expression in the pathogen at different stages of infection of themammalian host.

[0250] Use of the technology of the present invention enablesidentification of bacterial genes transcribed during infection,inhibitors of which would have utility in anti-bacterial therapy.Specific inhibitors of such gene transcription or of the subsequenttranslation of the resultant mRNA or of the function of thecorresponding expressed proteins would have utility in anti-bacterialtherapy.

[0251] The Determination of Expression During Infection of a Gene fromStreptococcus pneumoniae

[0252] Lung tissue from a 24 hr pneumonia infection of Streptococcuspneumoniae #100993 in the mouse is efficiently disrupted and processedin the presence of acid phenol and detergent to provide a mixture ofanimal and bacterial RNA. By freezing the tissue immediately in liquidnitrogen, and processing the tissue samples while still frozen, changesin the population of bacterial mRNA is minimized. The resultant totalRNA is free of DNA and protein (including RNAases and DNAases). Theoptimal conditions for disruption and processing to give high yields ofbacterial mRNA with transcripts of long length are followed by reversetranscribing the resulting mRNA to cDNA and amplified with ORF-specificprimers for a bacterial gene known to be expressed constitutively and atlow copy number. Aspects of this example II, part b, are modificationsof a published protocol (Cheung, et al.; Anal Biochem (1994)222:511-514).

[0253] a) Isolation of Lung Tissue Infected with Streptococcuspneumoniae #0100993 from a Mouse Respiratory Tract Infection Model.

[0254]Streptococcus pneumoniae # 100993 was seeded onto TSA (Tryptic SoyAgar, BBL) plates containing 5% horse blood and allowed to growovernight at 37° C. in a CO₂ incubator. Bacterial growth was scrapedinto 5 ml of phosphate-buffered saline (PBS) and adjusted to anA₆₀₀˜0.6(4×10⁶/ml). Mice (male CBA/J-1 mice, approximately 20 g) wereanaesthetized with isoflurane and 50 microliters of the preparedbacterial inoculum was delivered by intranasal instillation. Animalswere allowed to recover and observed twice daily for signs ofmoribundancy. Forty-eight hours after infection the animals wereeuthanized by carbon dioxide overdose and their torsos swabbed withethanol and then RNAZap. The torso was then opened, and the lungs wereaseptically removed. Half of each pair of lungs was placed in a cryovialand immediately frozen in liquid nitrogen; the other half was used forbacterial enumeration after homogenization of the tissue in 1 ml of PBS.

[0255] b) Isolation of Streptococcus pneumoniae #0100993 RNA fromInfected Tissue Samples

[0256] Infected tissue samples, in 2-ml cryo-strorage tubes, are removedfrom liquid nitrogen storage for immediate processing of the frozentissue. In a microbiological safety cabinet the samples are disrupted upto eight at a time. To disrupt the bacteria within the tissue sample,50-100 mg of the tissue is transfered to a FastRNA tube containing asilica/ceramic matrix (BIO101) Immediately, 1 ml of extraction reagents(FastRNA reagents, BIO101) are added to give a sample to reagent volumeratio of approximately 1 to 20. The tubes are shaken in a reciprocatingshaker (FastPrep FP120, BIO101) ata setting of 5.5 to 6 for 20-120 sec.The crude RNA preparation is extracted with chloroform/isoamyl alcohol,and precipitated with DEPC-treated/Isopropanol Precipitation Solution(BIO101). RNA preparations are stored in this isopropanol solution at−80° C. if necessary. The RNA is pelleted (12,000 g for 10 min.), washedwith 75% ethanol (v/v in DEPC-treated water), air-dried for 5-10 min,and resuspended in 0.1 ml of DEPC-treated water.

[0257] Quality of the RNA isolated is assessed by the ability to detectbacterial transcripts up to 2 kb in length by RT-PCR (as described belowin section). To demonstrate the isolation of bacterial RNA from theinfected tissue, samples of RNA are reverse transcribed, and thepresence of a constitutively expressed gene is detected through the useof quantitative PCR in the presence of a TaqMan probe (as describedbelow).

[0258] c) The Removal of DNA from Streptococcus pneumoniae(0100993)-derived RNA

[0259] DNA was removed from 50 microgram samples of RNA by a 30 minutetreatment at 37° C. with 10 units of RNAase-free DNAaseI (GeneHunter) inthe buffer supplied in a final volume of 57 microliters.

[0260] The DNAase was inactivated and removed by phenol:chloroformextraction. RNA was precipitated with 5 microliters of 3 M NaOAc and 200microliters 100% EtOH, and pelleted by centrifugation at 12,000 g for 10minutes. The RNA is pelleted (12,000g for 10 min.), washed with 75%ethanol (v/v in DEPC-treated water), air-dried for 5-10 min, andresuspended in 10-20 microliters of DEPC-treated water. RNA yield isquantitated by OD₂₆₀ after 1:1000 dilution of the cleaned RNA sample.RNA is stored at −80° C. if necessary and reverse-transcribed within oneweek.

[0261] d) The Preparation of cDNA from RNA Samples Derived from InfectedTissue

[0262] 10 microliter samples of DNAase treated RNA are reversetranscribed using a SuperScript Preamplification System for First StrandcDNA Synthesis kit (Gibco BRL, Life Technologies) according to themanufacturers instructions. 1 nanogram of random hexamers is used toprime each reaction. Controls without the addition of SuperScriptIIreverse transcriptase are also run. Both +/−RT samples are treated withRNaseH before proceeding to the PCR reaction.

[0263] e) The Use of PCR to Determine the Quality of Bacterial RNADerived from Infected Tissue

[0264] Long transcripts, which are expected to be of low copy numberwithin the bacterial cell, such as penicillin-binding protein 2 (PBP2),are reverse transcribed with random primers as described above andamplified by the following PCR method using ORF-specific primers, inorder to ascertain the quality, represented by length amplified, of themRNA obtained during extraction and purification.

[0265] PCR reactions are set up on ice in 0.2 ml tubes in a total volumeof 50 ul by adding the following components [final concentration]:AmpliTaq PCR Buffer II (1×), 1.5 mM MgCL₂, 1 mM dNTPs, 0.5 uM forwardprimer, 0.5 uM reverse primer, and 2 ul reverse-transcribed RNA. PCRreactions are run on a PE GeneAmp PCR System 9600 with an initial stepof 94° C. for 2 min, followed by 35 cycles of 94° C. for 30 sec, 42° C.for 30 sec and 72° C. for 30 sec, followed by a final extensison at 72°C. for 7 min.

[0266] f) The Use of PCR to Determine the Presence of a Bacterial cDNASpecies

[0267] PCR reactions are set up as described above using 0.5 microM eachof the ORF specific forward and reverse primers.

[0268] PCR product in 20 microliter aliquots are separated byelectrophoresis through 1 to 15% 1× TBE agarose gels or 10% 1× TBEacrylamide gels. PCR product is visualized by staining the gel withethidium bromide. Size estimates are made by comparison to a 100 bp DNALadder (Gibco BPL, Life Technologies). Alternatively, if the PCRproducts are conveniently labelled by, the use of a labelled PCR primer(e.g. labelled at the 5′end with a dye) a suitable aliquot of the PCRproduct is run out on a polyacrylamide sequencing gel and its presenceand quantity detected using a suitable gel scanning system (e.g. ABIPrism™ 377 Sequencer using GeneScan™ software as supplied by PerkinElmer).

[0269] RT/PCR controls may include +/− reverse transcriptase reactions,16s rRNA primers or DNA specific primer pairs designed to produce PCRproducts from non-transcribed Streptococcus pneumoniae #100993 genomicsequences.

[0270] To test the efficiency of the primer pairs they are used in DNAPCR with Streptococcus pneumoniae #100993 total DNA. PCR reactions areset up and run as described above using approx. 1 microgram of DNA inplace of the cDNA and 35 cycles of PCR.

[0271] Primer pairs which fail to give the predicted sized product ineither DNA PCR or RT/PCR are PCR failures and as such are uninformative.Of those which give the correct size product with DNA PCR two classesare distinguished in RT/PCR: 1.Genes which are not transcribed in vivoreproducibly fail to give a product in RT/PCR; and 2.Genes which aretranscribed in vivo reproducibly give the correct size product in RTIPCRand show a stronger signal in the +RT samples than the signal (if at allpresent) in −RT controls.

[0272] g) The Use of PCR and Fluorogenic Probes to Determine thePresence of a Bacterial cDNA Species

[0273] Specific sequence detection occurs by amplification of targetsequences in the PE Applied Biosystems 7700 Sequence Detection System inthe presence of an oligonucleotide probe labeled at the 5′ and 3′ endswith a reporter and quencher fluorescent dye, respectively (FQ probe),which anneals between the two PCR primers. Only specific product will bedetected when the probe is bound between the primers. As PCRamplification proceeds, the 5′-nuclease activity of Taq polymeraseinitially cleaves the reporter dye from the probe. The signal generatedwhen the reporter dye is physically separated from the quencher dye isdetected by measuring the signal with an attached CCD camera. Eachsignal generated equals one probe cleaved which corresponds toamplification of one target strand

[0274] PCR reactions are set up using the PE Applied Biosystem TaqManPCR Core Reagent Kit according to the instructions supplied such thateach reaction contains 5 microliters 10× PCR Buffer II, 7 microliters 25mM MgCl₂, 5 microliters 300 nM forward primer, 5 microliters reverseprimer, 5 microliters specific FQ probe, 1 microliter each 10 mM DATP,10 mM dCTP, 10 mM dGTP and 20 mM dUTP, 13.25 microliters distilledwater, 0.5 microliters AmpErase UNG, and 0.25 microliters AmpliTaq DNApolymerase to give a total volume of 45 microliters.

[0275] Amplification proceeds under the following thermal cyclingconditions: 50° C. hold for 2 minutes, 95° C. hold for 10 minutes, 40cycles of 95° C. for 15 seconds and 60° C. for 1 minute, followed by a25° C. hold until sample is retrieved. Detection occurs real-time. Datais collected at the end of the reaction

[0276] Two polynucleotide sequences of the invention, SEQ ID NOS:1 and3, were identified in the above test as transcribed in vivo. SEQ ID NO:2was deduced from the polynucleotide sequence given as SEQ ID NO:1. SEQID NO.4 was deduced from the polynucleotide sequence given as SEQ IDNO:3. The pair of PCR primers used to identify the gene are given as SEQID NOS:5 and 6.

1 6 2100 base pairs nucleic acid double linear 1 GAGGATATCC AGCTAGTTCCAGCCTTTTTA AAAACGGCCC TACCAGATTG GGAAGGCCAA 60 CTAAGACACA TTCATCTTGAGGAATAGGAG AGAAACATGA CTTATCATTT TACTGAAGAA 120 TACGATATTA TTGTAATTGGTGCGGGACAC GCTGGGGTTG AGGCTTCCTT GGCCGCTAGC 180 CGTATGGGCT GTAAGGTCCTGCTTGCGACC ATCAATATTG AAATGCTGGC TTTCATGCCT 240 TGTAATCCCT CTATCGGTGGTTCTGCTAAG GGGATTGTCG TACGTGAAGT CGATGCCCTC 300 GGTGGCGAGA TGGCCAAGACCATTGACAAG ACTTACATCC AGATGAAGAT GCTCAACACA 360 GGGAAGGGCC CAGCCGTTCGTGCCCTTCGT GCGCAGGCTG ATAAGGAACT TTACTCTAAG 420 GAAATGCGCA AGACAGTTGAAAATCAAGAA AATCTGACCC TTCGTCAAAC CATGATTGAT 480 GAGATTTTGG TGGAAGATGGCAAGGTTGTC GGTGTGCGTA CAGCCACCCA TCAAGAATAT 540 GCTGCTAAGG CTGTTATTGTGACGACAGGG ACTGCTCTCC GTGGGGAAAT TATCATCGGA 600 GACCTCAAGT ACTCATCAGGTTCTAACCAC AGCTTGGCTT CTATTAACCT AGCTGACAAT 660 CTCAAGGAAC TGGGTCTCGAAATCGGTCGT TTCAAGACAG GAACCCCTCC ACGTGTCAAG 720 GCTTCTTCTA TCAATTACGATGTGACGGAA ATTCAGCCAG GAGACGAAGT GCCTAATCAT 780 TTCTCATACA CTTCACGTGATGAGGATTAT GTCAAAGATC AAGTGCCATG CTGGTTGACC 840 TATACCAATG GTACCAGTCATGAGATTATC CAAAACAACC TCCACCGTGC GCCTATGTTT 900 ACAGGTGTGG TCAAGGGAGTGGGGCCTCGT TACTGTCCGT CGATTGAAGA CAAGATTGTG 960 CGCTTTGCGG ACAAGGAACGTCACCAACTC TTCCTTGAGC CAGAAGGACG CAATACTGAG 1020 GAAGTCTATG TTCAAGGACTTTCAACCAGT CTGCCTGAGG ATGTCCAGCG TGACTTGGTT 1080 CATTCCATCA AAGGTTTGGAAAATGCAGAG ATGATGCGGA CAGGTTATGC TATTGAGTAT 1140 GATATGGTCT TGCCTCATCAGTTGCGTGCG ACTTTGGAAA CCAAGAAAAT CTCAGGTCTC 1200 TTCACTGCTG GTCAGACAAATGGAACATCA GGTTATGAAG AAGCTGCTGG CCAAGGGATT 1260 ATCGCGGGTA TCAATGCGGCTCTGAAAATC CAAGGTAAAC CTGAGTTGAT TCTAAAACGA 1320 AGTGACGGTT ATATCGGGGTGATGATCGAC GACTTGGTGA CCAAGGGAAC CATTGAACCT 1380 TACCGTCTCT TGACCAGTCGTGCTGAATAC CGTCTCATTC TTCGTCATGA CAATGCTGAT 1440 ATGCGCTTGA CTGAGATGGGACGCGAGATT GGCCTTGTGG ATGATGAACG CTGGGCTCGT 1500 TTTGAAATCA AGAAAAATCAATTTGATAAT GAGATGAAAC GCCTAGACAG TATCAAACTC 1560 AAGCCAGTCA AGGAAACCAATGCTAAGGTT GAGGAAATGG GCTTCAAGCC GTTGACAGAT 1620 GCGGTGACAG CCAAAGAATTCCTTCGCCGT CCAGAAGTTT CTTACCAAGA TGTGGTGGCC 1680 TTCATCGGAC CAGCTGCAGAAGACTTGGAT GACAAGATTA TCGAATTGAT TGAAACAGAA 1740 ATCAAGTACG AAGGCTATATTTCAAAAGCC ATGGATCAGG TTGCCAAGAT GAAACGTATG 1800 GAAGAAAAAC GCATTCCAGCCAATATTGAC TGGGATGACA TCGATTCTAT TGCGACGGAA 1860 GCTCGTCAGA AGTTCAAACTCATCAATCCA GAAACCATCG GCCAAGCCAG CCGTATTTCG 1920 GGAGTAAACC CAGCAGATATTTCTATTTTG ATGGTGTATC TGGAAGGTAA AAATCGTAGT 1980 ATTTCTAAAA CTCTTCAAAAATCAAAATGA TACGTCGTCG GCTTCTTACG AATGAGTTCA 2040 AAGCTTGGCT TTGATTCATCTCCAGCCTCC CATAGTTCCC CGAACTATGG GAGCTAACTC 2100 637 amino acids aminoacid single linear 2 Met Thr Tyr His Phe Thr Glu Glu Tyr Asp Ile Ile ValIle Gly Ala 1 5 10 15 Gly His Ala Gly Val Glu Ala Ser Leu Ala Ala SerArg Met Gly Cys 20 25 30 Lys Val Leu Leu Ala Thr Ile Asn Ile Glu Met LeuAla Phe Met Pro 35 40 45 Cys Asn Pro Ser Ile Gly Gly Ser Ala Lys Gly IleVal Val Arg Glu 50 55 60 Val Asp Ala Leu Gly Gly Glu Met Ala Lys Thr IleAsp Lys Thr Tyr 65 70 75 80 Ile Gln Met Lys Met Leu Asn Thr Gly Lys GlyPro Ala Val Arg Ala 85 90 95 Leu Arg Ala Gln Ala Asp Lys Glu Leu Tyr SerLys Glu Met Arg Lys 100 105 110 Thr Val Glu Asn Gln Glu Asn Leu Thr LeuArg Gln Thr Met Ile Asp 115 120 125 Glu Ile Leu Val Glu Asp Gly Lys ValVal Gly Val Arg Thr Ala Thr 130 135 140 His Gln Glu Tyr Ala Ala Lys AlaVal Ile Val Thr Thr Gly Thr Ala 145 150 155 160 Leu Arg Gly Glu Ile IleIle Gly Asp Leu Lys Tyr Ser Ser Gly Ser 165 170 175 Asn His Ser Leu AlaSer Ile Asn Leu Ala Asp Asn Leu Lys Glu Leu 180 185 190 Gly Leu Glu IleGly Arg Phe Lys Thr Gly Thr Pro Pro Arg Val Lys 195 200 205 Ala Ser SerIle Asn Tyr Asp Val Thr Glu Ile Gln Pro Gly Asp Glu 210 215 220 Val ProAsn His Phe Ser Tyr Thr Ser Arg Asp Glu Asp Tyr Val Lys 225 230 235 240Asp Gln Val Pro Cys Trp Leu Thr Tyr Thr Asn Gly Thr Ser His Glu 245 250255 Ile Ile Gln Asn Asn Leu His Arg Ala Pro Met Phe Thr Gly Val Val 260265 270 Lys Gly Val Gly Pro Arg Tyr Cys Pro Ser Ile Glu Asp Lys Ile Val275 280 285 Arg Phe Ala Asp Lys Glu Arg His Gln Leu Phe Leu Glu Pro GluGly 290 295 300 Arg Asn Thr Glu Glu Val Tyr Val Gln Gly Leu Ser Thr SerLeu Pro 305 310 315 320 Glu Asp Val Gln Arg Asp Leu Val His Ser Ile LysGly Leu Glu Asn 325 330 335 Ala Glu Met Met Arg Thr Gly Tyr Ala Ile GluTyr Asp Met Val Leu 340 345 350 Pro His Gln Leu Arg Ala Thr Leu Glu ThrLys Lys Ile Ser Gly Leu 355 360 365 Phe Thr Ala Gly Gln Thr Asn Gly ThrSer Gly Tyr Glu Glu Ala Ala 370 375 380 Gly Gln Gly Ile Ile Ala Gly IleAsn Ala Ala Leu Lys Ile Gln Gly 385 390 395 400 Lys Pro Glu Leu Ile LeuLys Arg Ser Asp Gly Tyr Ile Gly Val Met 405 410 415 Ile Asp Asp Leu ValThr Lys Gly Thr Ile Glu Pro Tyr Arg Leu Leu 420 425 430 Thr Ser Arg AlaGlu Tyr Arg Leu Ile Leu Arg His Asp Asn Ala Asp 435 440 445 Met Arg LeuThr Glu Met Gly Arg Glu Ile Gly Leu Val Asp Asp Glu 450 455 460 Arg TrpAla Arg Phe Glu Ile Lys Lys Asn Gln Phe Asp Asn Glu Met 465 470 475 480Lys Arg Leu Asp Ser Ile Lys Leu Lys Pro Val Lys Glu Thr Asn Ala 485 490495 Lys Val Glu Glu Met Gly Phe Lys Pro Leu Thr Asp Ala Val Thr Ala 500505 510 Lys Glu Phe Leu Arg Arg Pro Glu Val Ser Tyr Gln Asp Val Val Ala515 520 525 Phe Ile Gly Pro Ala Ala Glu Asp Leu Asp Asp Lys Ile Ile GluLeu 530 535 540 Ile Glu Thr Glu Ile Lys Tyr Glu Gly Tyr Ile Ser Lys AlaMet Asp 545 550 555 560 Gln Val Ala Lys Met Lys Arg Met Glu Glu Lys ArgIle Pro Ala Asn 565 570 575 Ile Asp Trp Asp Asp Ile Asp Ser Ile Ala ThrGlu Ala Arg Gln Lys 580 585 590 Phe Lys Leu Ile Asn Pro Glu Thr Ile GlyGln Ala Ser Arg Ile Ser 595 600 605 Gly Val Asn Pro Ala Asp Ile Ser IleLeu Met Val Tyr Leu Glu Gly 610 615 620 Lys Asn Arg Ser Ile Ser Lys ThrLeu Gln Lys Ser Lys 625 630 635 1871 base pairs nucleic acid doublelinear 3 GGTGCGGGAC ACGCTGGGGT TGAGGCTTCC TTGGCCGCTA GCCGTATGGGCTGTAAGGTC 60 CTGCTTGCGA CCATCAATAT TGAAATGCTG GCTTTCATGC CTTGTAATCCCTCTATCGGT 120 GGTTCTGCTA AGGGGATTGT CGTACGTGAA GTCGATGCCC TCGGTGGCGAGATGGCCAAG 180 ACCATTGACA AGACTTACAT CCAGATGAAG ATGCTCAACA CAGGGAAGGGCCCAGCCGTT 240 CGTGCCCTTC GTGCGCAGGC TGATAAGGAA CTTTACTCTA AGGAAATGCGCAAGACAGTT 300 GAAAATCAAG AAAATCTGAC CCTTCGTCAA ACCATGATTG ATGAGATTTTGGTGGAAGAT 360 GGCAAGGTTG TCGGTGTGCG TACAGCCACC CATCAAGAAT ATGCTGCTAAGGCTGTTATT 420 GTGACGACAG GGACTGCTCT CCGTGGGGAA ATTATCATCG GAGACCTCAAGTACTCATCA 480 GGTTCTAACC ACAGCTTGGC TTCTATTAAC CTAGCTGACA ATCTCAAGGAACTGGGTCTC 540 GAAATCGGTC GTTTCAAGAC AGGAACCCCT CCACGTGTCA AGGCTTCTTCTATCAATTAC 600 GATGTGACGG AAATTCAGCC AGGAGACGAA GTGCCTAATC ATTTCTCATACACTTCACGT 660 GATGAGGATT ATGTCAAAGA TCAAGTGCCA TGCTGGTTGA CCTATACCAATGGTACCAGT 720 CATGAGATTA TCCAAAACAA CCTCCACCGT GCGCCTATGT TTACAGGTGTGGTCAAGGGA 780 GTGGGGCCTC GTTACTGTCC GTCGATTGAA GACAAGATTG TGCGCTTTGCGGACAAGGAA 840 CGTCACCAAC TCTTCCTTGA GCCAGAAGGA CGCAATACTG AGGAAGTCTATGTTCAAGGA 900 CTTTCAACCA GTCTGCCTGA GGATGTCCAG CGTGACTTGG TTCATTCCATCAAAGGTTTG 960 GAAAATGCAG AGATGATGCG GACAGGTTAT GCTATTGAGT ATGATATGGTCTTGCCTCAT 1020 CAGTTGCGTG CGACTTTGGA AACCAAGAAA ATCTCAGGTC TCTTCACTGCTGGTCAGACA 1080 AATGGAACAT CAGGTTATGA AGAAGCTGCT GGCCAAGGGA TTATCGCGGGTATCAATGCG 1140 GCTCTGAAAA TCCAAGGTAA ACCTGAGTTG ATTCTAAAAC GAAGTGACGGTTATATCGGG 1200 GTGATGATCG ACGACTTGGT GACCAAGGGA ACCATTGAAC CTTACCGTCTCTTGACCAGT 1260 CGTGCTGAAT ACCGTCTCAT TCTTCGTCAT GACAATGCTG ATATGCGCTTGACTGAGATG 1320 GGACGCGAGA TTGGCCTTGT GGATGATGAA CGCTGGGCTC GTTTTGAAATCAAGAAAAAT 1380 CAATTTGATA ATGAGATGAA ACGCCTAGAC AGTATCAAAC TCAAGCCAGTCAAGGAAACC 1440 AATGCTAAGG TTGAGGAAAT GGGCTTCAAG CCGTTGACAG ATGCGGTGACAGCCAAAGAA 1500 TTCCTTCGCC GTCCAGAAGT TTCTTACCAA GATGTGGTGG CCTTCATCGGACCAGCTGCA 1560 GAAGACTTGG ATGACAAGAT TATCGAATTG ATTGAAACAG AAATCAAGTACGAAGGGTAT 1620 ATTTCAAAAG CCATGGATCA GGTTGGCAAG ATGAAACGTA TGGAAGAAAAACGCATTCCA 1680 GCCAATATTG ACTGGGATGA CATCGATTCT ATTGGGACGG AAGCTCGTCAGAAGTTCAAA 1740 CTCATCAATC CAGAAACCAT CGGGCAAGCC AGCCGTATTT CGGGAGTTAACCCAGCAGAT 1800 ATTTCTATTT TGATGGTGTA TCTGGAAGGT AAAAATCGTA GTATTTCTAAAACTCCTCCA 1860 AAATCAAAAT G 1871 623 amino acids amino acid singlelinear 4 Gly Ala Gly His Ala Gly Val Glu Ala Ser Leu Ala Ala Ser Arg Met1 5 10 15 Gly Cys Lys Val Leu Leu Ala Thr Ile Asn Ile Glu Met Leu AlaPhe 20 25 30 Met Pro Cys Asn Pro Ser Ile Gly Gly Ser Ala Lys Gly Ile ValVal 35 40 45 Arg Glu Val Asp Ala Leu Gly Gly Glu Met Ala Lys Thr Ile AspLys 50 55 60 Thr Tyr Ile Gln Met Lys Met Leu Asn Thr Gly Lys Gly Pro AlaVal 65 70 75 80 Arg Ala Leu Arg Ala Gln Ala Asp Lys Glu Leu Tyr Ser LysGlu Met 85 90 95 Arg Lys Thr Val Glu Asn Gln Glu Asn Leu Thr Leu Arg GlnThr Met 100 105 110 Ile Asp Glu Ile Leu Val Glu Asp Gly Lys Val Val GlyVal Arg Thr 115 120 125 Ala Thr His Gln Glu Tyr Ala Ala Lys Ala Val IleVal Thr Thr Gly 130 135 140 Thr Ala Leu Arg Gly Glu Ile Ile Ile Gly AspLeu Lys Tyr Ser Ser 145 150 155 160 Gly Ser Asn His Ser Leu Ala Ser IleAsn Leu Ala Asp Asn Leu Lys 165 170 175 Glu Leu Gly Leu Glu Ile Gly ArgPhe Lys Thr Gly Thr Pro Pro Arg 180 185 190 Val Lys Ala Ser Ser Ile AsnTyr Asp Val Thr Glu Ile Gln Pro Gly 195 200 205 Asp Glu Val Pro Asn HisPhe Ser Tyr Thr Ser Arg Asp Glu Asp Tyr 210 215 220 Val Lys Asp Gln ValPro Cys Trp Leu Thr Tyr Thr Asn Gly Thr Ser 225 230 235 240 His Glu IleIle Gln Asn Asn Leu His Arg Ala Pro Met Phe Thr Gly 245 250 255 Val ValLys Gly Val Gly Pro Arg Tyr Cys Pro Ser Ile Glu Asp Lys 260 265 270 IleVal Arg Phe Ala Asp Lys Glu Arg His Gln Leu Phe Leu Glu Pro 275 280 285Glu Gly Arg Asn Thr Glu Glu Val Tyr Val Gln Gly Leu Ser Thr Ser 290 295300 Leu Pro Glu Asp Val Gln Arg Asp Leu Val His Ser Ile Lys Gly Leu 305310 315 320 Glu Asn Ala Glu Met Met Arg Thr Gly Tyr Ala Ile Glu Tyr AspMet 325 330 335 Val Leu Pro His Gln Leu Arg Ala Thr Leu Glu Thr Lys LysIle Ser 340 345 350 Gly Leu Phe Thr Ala Gly Gln Thr Asn Gly Thr Ser GlyTyr Glu Glu 355 360 365 Ala Ala Gly Gln Gly Ile Ile Ala Gly Ile Asn AlaAla Leu Lys Ile 370 375 380 Gln Gly Lys Pro Glu Leu Ile Leu Lys Arg SerAsp Gly Tyr Ile Gly 385 390 395 400 Val Met Ile Asp Asp Leu Val Thr LysGly Thr Ile Glu Pro Tyr Arg 405 410 415 Leu Leu Thr Ser Arg Ala Glu TyrArg Leu Ile Leu Arg His Asp Asn 420 425 430 Ala Asp Met Arg Leu Thr GluMet Gly Arg Glu Ile Gly Leu Val Asp 435 440 445 Asp Glu Arg Trp Ala ArgPhe Glu Ile Lys Lys Asn Gln Phe Asp Asn 450 455 460 Glu Met Lys Arg LeuAsp Ser Ile Lys Leu Lys Pro Val Lys Glu Thr 465 470 475 480 Asn Ala LysVal Glu Glu Met Gly Phe Lys Pro Leu Thr Asp Ala Val 485 490 495 Thr AlaLys Glu Phe Leu Arg Arg Pro Glu Val Ser Tyr Gln Asp Val 500 505 510 ValAla Phe Ile Gly Pro Ala Ala Glu Asp Leu Asp Asp Lys Ile Ile 515 520 525Glu Leu Ile Glu Thr Glu Ile Lys Tyr Glu Gly Tyr Ile Ser Lys Ala 530 535540 Met Asp Gln Val Gly Lys Met Lys Arg Met Glu Glu Lys Arg Ile Pro 545550 555 560 Ala Asn Ile Asp Trp Asp Asp Ile Asp Ser Ile Gly Thr Glu AlaArg 565 570 575 Gln Lys Phe Lys Leu Ile Asn Pro Glu Thr Ile Gly Gln AlaSer Arg 580 585 590 Ile Ser Gly Val Asn Pro Ala Asp Ile Ser Ile Leu MetVal Tyr Leu 595 600 605 Glu Gly Lys Asn Arg Ser Ile Ser Lys Thr Pro ProLys Ser Lys 610 615 620 20 base pairs nucleic acid single linear 5ATGACTTATC ATTTTACTGA 20 20 base pairs nucleic acid single linear 6TCATTTTGAT TTTTGAAGAG 20

What is claimed is: 1 An isolated polypeptide selected from the groupconsisting of: (i) an isolated polypeptide comprising an amino acidhaving at least: (a) 70% identity; (b) 80% identity; (c) 90% identity;or (d) 95% identity to the amino acid sequence of SEQ ID NO:2 or 4 overthe entire length of SEQ ID NO:2 or 4; (ii) an isolated polypeptidecomprising the amino acid sequence of SEQ ID NO:2 or 4, (iii) anisolated polypeptide which is the amino acid sequence of SEQ ID NO:2 or4, and (iv) a polypeptide which is encoded by a recombinantpolynucleotide comprising the polynucleotide sequence of SEQ ID NO:1 or3.
 2. An isolated polynucleotide selected from the group consisting of:(i) an isolated polynucleotide comprising a polynucleotide sequenceencoding a polypeptide that has at least (a) 70% identity; (b) 80%identity; (c) 90% identity; or (d) 95% identity; to the amino acidsequence of SEQ ID NO:2 or 4, over the entire length of SEQ ID NO:2 or4; (ii) an isolated polynucleotide comprising a polynucleotide sequencethat has at least: (a) 70% identity (b) 80% identity; (c) 90% identity,or (d) 95% identity; over its entire length to a polynucleotide sequenceencoding the polypeptide of SEQ ID NO.2or 4; (iii) an isolatedpolynucleotide comprising a nucleotide sequence which has at least: (a)70% identity; (b) 80% identity; (c) 90% identity; or (d) 95% identity;to that of SEQ ID NO: 1 or 3 over the entire length of SEQ ID NO:1 or 3;(iv) an isolated polynucleotide comprising a nucleotide sequenceencoding the polypeptide of SEQ ID NO:2 or 4; (v) an isolatedpolynucleotide which is the polynucleotide of SEQ ID NO: 1 or 3; (vi) anisolated polynucleotide obtainable by screening an appropriate libraryunder stringent hybridization conditions with a probe having thesequence of SEQ ID NO: 1 or 3 or a fragment thereof; (vii) an isolatedpolynucleotide encoding a mature polypeptide expressed by the gidA1 genecontained in the Streptococcus pneumoniae; and (viii) a polynucleotidesequence complementary to said isolated polynucleotide of (i), (ii),(iii), (iv), (v), (vi) or (vii).
 3. An antibody antigenic to orimmunospecific for the polypeptide of claim
 1. 4. A method for thetreatment of an individual: (i) in need of enhanced activity orexpression of the polypeptide of claim 1 comprising the step of: (a)administering to the individual a therapeutically effective amount of anagonist to said polypeptide; or (b) providing to the individual anisolated polynucleotide comprising a polynucleotide sequence encodingsaid polypeptide in a form so as to effect production of saidpolypeptide activity in vivo; or (ii) having need to inhibit activity orexpression of the polypeptide of claim 1 comprising: (a) administeringto the individual a therapeutically effective amount of an antagonist tosaid polypeptide; or (b) administering to the individual a nucleic acidmolecule that inhibits the expression of a polynucleotide sequenceencoding said polypeptide; or (c) administering to the individual atherapeutically effective amount of a polypeptide that competes withsaid polypeptide for its ligand, substrate, or receptor.
 5. A processfor diagnosing or prognosing a disease or a susceptibility to a diseasein an individual related to expression or activity of the polypeptide ofclaim 1 in an individual comprising the step of: (a) determining thepresence or absence of a mutation in the nucleotide sequence encodingsaid polypeptide in the genome of said individual; or (b) analyzing forthe presence or amount of said polypeptide expression in a samplederived from said individual.
 6. A method for screening to identifycompounds that activate or that inhibit the function of the polypeptideof claim 1 which comprises a method selected from the group consistingof: (a) measuring the binding of a candidate compound to the polypeptideor to the cells or membranes bearing the polypeptide or a fusion proteinthereof by means of a label directly or indirectly associated with thecandidate compound; (b) measuring the binding of a candidate compound tothe polypeptide or to the cells or membranes bearing the polypeptide ora fusion protein thereof in the presence of a labeled competitor; (c)testing whether the candidate compound results in a signal generated byactivation or inhibition of the polypeptide, using detection systemsappropriate to the cells or cell membranes bearing the polypeptide; (d)mixing a candidate compound with a solution containing a polypeptide ofclaim 1, to form a mixture, measuring activity of the polypeptide in themixture, and comparing the activity of the mixture to a standard; (e)detecting the effect of a candidate compound on the production of mRNAencoding said polypeptide and said polypeptide in cells, using forinstance, an ELISA assay, or (f) (1) contacting a composition comprisingthe polypeptide with the compound to be screened under conditions topermit interaction between the compound and the polypeptide to assessthe interaction of a compound, such interaction being associated with asecond component capable of providing a detectable signal in response tothe interaction of the polypeptide with the compound; and (2)determining whether the compound interacts with and activates orinhibits an activity of the polypeptide by detecting the presence orabsence of a signal generated from the interaction of the compound withthe polypeptide.
 7. An agonist or an antagonist of the activity orexpression polypeptide of claim
 1. 8. An expression system comprising apolynucleotide capable of producing a polypeptide of claim 1 when saidexpression system is present in a compatible host cell. 9 A host cellcomprising the expression system of claim 8 or a membrane thereofexpressing a polypeptide selected from the group consisting of: (i) anisolated polypeptide comprising an amino acid sequence selected from thegroup having at least: (a) 70% identity; (b) 80% identity; (c) 90%identity; or (d) 95% identity to the amino acid sequence of SEQ ID NO:2or 4 over the entire length of SEQ ID NO:2 or 4; (ii) an isolatedpolypeptide comprising the amino acid sequence of SEQ ID NO:2 or 4;(iii) an isolated polypeptide which is the amino acid sequence of SEQ IDNO:2 or 4, and (iv) a polypeptide which is encoded by a recombinantpolynucleotide comprising the polynucleotide sequence of SEQ ID NO:1 or3.
 10. A process for producing a polypeptide selected from the groupconsisting of: (i) an isolated polypeptide comprising an amino acidsequence selected from the group having at least: (a) 70% identity; (b)80% identity; (c) 90% identity; or (d) 95% identity to the amino acidsequence of SEQ ID NO:2 or 4 over the entire length of SEQ ID NO:2 or 4;(ii) an isolated polypeptide comprising the amino acid sequence of SEQID NO:2 or 4; (iii) an isolated polypeptide which is the amino acidsequence of SEQ ID NO:2 or 4, and (iv) a polypeptide which is encoded bya recombinant polynucleotide comprising the polynucleotide sequence ofSEQ ID NO:1 or 3, comprising the step of culturing a host cell of claim9 under conditions sufficient for the production of said polypeptide.11. A process for producing a host cell comprising the expression systemof claim 8 or a membrane thereof expressing a polypeptide selected fromthe group consisting of: (i) an Isolated polypeptide comprising an aminoacid sequence selected from the group having at least: (a) 70% identity;(b) 80% identity; (c) 90% identity; or (d) 95% identity to the aminoacid sequence of SEQ ID NO:2 or 4 over the entire length of SEQ ID NO:2or 4; (ii) an isolated polypeptide comprising the amino acid sequence ofSEQ ID NO:2 or 4; (iii) an isolated polypeptide which is the amino acidsequence of SEQ ID NO:2 or 4, and (iv) a polypeptide which is encoded bya recombinant polynucleotide comprising the polynucleotide sequence ofSEQ ID NO:1 or 3, said process comprising the step of transforming ortransfecting a cell with an expression system comprising apolynucleotide capable of producing said polypeptide of (i), (ii), (iii)or (iv) when said expression system is present in a compatible host cellsuch the host cell, under appropriate culture conditions, produces saidpolypeptide of (i), (ii), (iii) or (iv).
 12. A host cell produced by theprocess of claim 11 or a membrane thereof expressing a polypeptideselected from the group consisting of: (i) an isolated polypeptidecomprising an amino acid sequence selected from the group having atleast: (a) 70% identity; (b) 80% identity; (c) 90% identity; or (d) 95%identity to the amino acid sequence of SEQ ID NO:2 or 4 over the entirelength of SEQ ID NO:2 or 4; (ii) an isolated polypeptide comprising theamino acid sequence of SEQ ID NO:2 or 4; (iii) an isolated polypeptidewhich is the amino acid sequence of SEQ ID NO:2 or 4, and (iv) apolypeptide which is encoded by a recombinant polynucleotide comprisingthe polynucleotide sequence of SEQ ID NO:1 or
 3. 13 A computer readablemedium having stored thereon a member selected from the group consistingof: a polynucleotide comprising the sequence of SEQ ID NO: 1 or 3; apolypeptide comprising the sequence of SEQ ID NO: 2 or 4; a set ofpolynucleotide sequences wherein at least one of said sequencescomprises the sequence of SEQ ID NO: 1 or 3; a set of polypeptidesequences wherein at least one of said sequences comprises the sequenceof SEQ ID NO: 2 or 4; a data set representing a polynucleotide sequencecomprising the sequence of SEQ ID NO: 1 or 3; a data set representing apolynucleotide sequence encoding a polypeptide sequence comprising thesequence of SEQ ID NO: 2 or 4; a polynucleotide comprising the sequenceof SEQ ID NO: 1 or 3; a polypeptide comprising the sequence of SEQ IDNO: 2 or 4; a set of polynucleotide sequences wherein at least one ofsaid sequences comprises the sequence of SEQ ID NO: 1 or 3; a set ofpolypeptide sequences wherein at least one of said sequences comprisesthe sequence of SEQ ID NO: 2 or 4; a data set representing apolynucleotide sequence comprising the sequence of SEQ ID NO: 1 or 3; adata set representing a polynucleotide sequence encoding a polypeptidesequence comprising the sequence of SEQ ID NO: 2 or
 4. 14. A computerbased method for performing homology identification, said methodcomprising the steps of providing a polynucleotide sequence comprisingthe sequence of SEQ ID NO: 1 or 3 in a computer readable medium; andcomparing said polynucleotide sequence to at least one polynucleotide orpolypeptide sequence to identify homology.
 15. A further embodiment ofthe invention provides a computer based method for polynucleotideassembly, said method comprising the steps of: providing a firstpolynucleotide sequence comprising the sequence of SEQ ID NO: 1 or 3 ina computer readable medium; and screening for at least one overlappingregion between said first polynucleotide sequence and a secondpolynucleotide sequence.
 16. An isolated polynucleotide selected formthe group consisting of: (a) an isolated polynucleotide comprising anucleotide sequence which has at least 70%, 80%, 90%, 95%, 97% identityto SEQ ID NO:3 over the entire length of SEQ ID NO:3; (b) an isolatedpolynucleotide comprising the polynucleotide of SEQ ID NO:3; (c) thepolynucleotide of SEQ ID NO:3; or (d) an isolated polynucleotidecomprising a nucleotide sequence encoding a polypeptide which has atleast 70%, 80%, 90%, 95%, 97-99% identity to the amino acid sequence ofSEQ ID NO:4, over the entire length of SEQ ID NO:4.
 17. A polypeptideselected from the group consisting of: (a) a polypeptide which comprisesan amino acid sequence which has at least 70%, 80%, 90%, 95%. 97-99%identity to that of SEQ ID NO:4 over the entire length of SEQ ID NO:4;(b) a polypeptide which has an amino acid sequence which is at least70%, 80%, 90%, 95%, 97-99% identity to the amino acid sequence of SEQ IDNO:4 over the entire length of SEQ ID NO:4; (c) a polypeptide whichcomprises the amino acid of SEQ ID NO:4; (d) a polypeptide which is thepolypeptide of SEQ ID NO:4; (e) a polypeptide which is encoded by apolynucleotide comprising the sequence contained in SEQ ID NO:3.